From 96b560ac8b95ad3547534c97eb037027988e29c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:46 +0200 Subject: gnu: r-dearseq: Update to 1.8.4. * gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10b70bab06..81a272142d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2370,14 +2370,14 @@ (define-public r-cummerbund (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.1") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1")))) + "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl")))) (build-system r-build-system) (propagated-inputs (list r-compquadform -- cgit v1.2.3 From 29a947216c2bab9471504add000531811de9252a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:51 +0200 Subject: gnu: r-annotationforge: Update to 1.38.1. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81a272142d..55d358c748 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3279,14 +3279,14 @@ (define-public r-annotationfilter (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8")))) + "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From 15243c2f8458da002a2fb621b4e6c305ffc0dee3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:52 +0200 Subject: gnu: r-biostrings: Update to 2.64.1. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d358c748..bce4c030b0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3566,13 +3566,13 @@ (define-public r-biocparallel (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.0") + (version "2.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8")))) + "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From 038eeeaf2a521f943fa291610bf6a1740eb56b57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:52 +0200 Subject: gnu: r-chipseeker: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.1. [propagated-inputs]: Add r-ggvenndiagram. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bce4c030b0..c70c08936a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3698,13 +3698,13 @@ (define-public r-category (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7")))) + "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3718,6 +3718,7 @@ (define-public r-chipseeker r-genomicranges r-genomicfeatures r-ggplot2 + r-ggvenndiagram r-gplots r-gtools r-dplyr -- cgit v1.2.3 From c82320aa21a78fd5494ea9d8aa24b1f8ee6963ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:52 +0200 Subject: gnu: r-complexheatmap: Update to 2.12.1. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c70c08936a..02e417d98d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3771,14 +3771,14 @@ (define-public r-chipseq (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.0") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65")))) + "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) -- cgit v1.2.3 From ba6a3e7d39b2fe0dba38c16ee151f6115aa4a22f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:52 +0200 Subject: gnu: r-gage: Update to 2.46.1. * gnu/packages/bioconductor.scm (r-gage): Update to 2.46.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02e417d98d..1b89d751fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4211,14 +4211,14 @@ (define-public r-fastseg (define-public r-gage (package (name "r-gage") - (version "2.46.0") + (version "2.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b")))) + "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) -- cgit v1.2.3 From a15ad5ebe3ecbf9fb45b827086d5270db8bca4b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:52 +0200 Subject: gnu: r-genomeinfodb: Update to 1.32.4. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b89d751fe..cb330e90a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4329,13 +4329,13 @@ (define-public r-genomation (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "17nwcq2ivj3bdibdywfyjq4n6z0djispbh9ahqa55sp31ksq41xh")))) + "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From a16c87fae16334740cab2a17fad22ace64a7698f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:53 +0200 Subject: gnu: r-genomicfeatures: Update to 1.48.4. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb330e90a9..523e7a6c33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4389,13 +4389,13 @@ (define-public r-genomicalignments (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.3") + (version "1.48.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1")))) + "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 039d894b9d7e05e624a57eeae9e213fc717e8eb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:53 +0200 Subject: gnu: r-limma: Update to 3.52.4. * gnu/packages/bioconductor.scm (r-limma): Update to 3.52.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 523e7a6c33..a450e06bd5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4693,13 +4693,13 @@ (define-public r-lfa (define-public r-limma (package (name "r-limma") - (version "3.52.2") + (version "3.52.4") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65")))) + "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 309cfcedca91e56e613f92c68b345686226fcc73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:53 +0200 Subject: gnu: r-zellkonverter: Update to 1.6.5. * gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a450e06bd5..a3128b77e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6569,13 +6569,13 @@ (define-public r-zlibbioc (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.3") + (version "1.6.5") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz")))) + (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e581479be804490ad0f221cdd4532ade2206a71b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:53 +0200 Subject: gnu: r-diffbind: Update to 3.6.4. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3128b77e7..54aa7ca5ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6806,14 +6806,14 @@ (define-public r-greylistchip (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.1") + (version "3.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr")))) + "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 41f029c12a043b656d53bc68fdbe447977656509 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:53 +0200 Subject: gnu: r-scaledmatrix: Update to 1.4.1. * gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 54aa7ca5ff..de2cdc593a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7668,14 +7668,14 @@ (define-public r-biocneighbors (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl")))) + "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a047448aaddd5e6550b1aa3c0d2637609f1625da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:54 +0200 Subject: gnu: r-treeio: Update to 1.20.2. * gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index de2cdc593a..9f56f30163 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7694,14 +7694,14 @@ (define-public r-scaledmatrix (define-public r-treeio (package (name "r-treeio") - (version "1.20.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla")))) + "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1cb30ba7146e2e16e8cf869f1c723ff9534c0d1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:54 +0200 Subject: gnu: r-ggtree: Update to 3.4.4. * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f56f30163..76fe9b1c6b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7726,14 +7726,14 @@ (define-public r-treeio (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.0") + (version "3.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4")))) + "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2b4a7fa22ec57bb6023ae0fb7a28f4b1c0e47e1c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:54 +0200 Subject: gnu: r-residualmatrix: Update to 1.6.1. * gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76fe9b1c6b..0ebae95f15 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8216,14 +8216,14 @@ (define-public r-icobra (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4")))) + "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) -- cgit v1.2.3 From 842431a036e8d9bff6519c0ad2c7986122e50bac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:54 +0200 Subject: gnu: r-dose: Update to 3.22.1. * gnu/packages/bioconductor.scm (r-dose): Update to 3.22.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ebae95f15..f606439884 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9350,14 +9350,14 @@ (define-public r-fgsea (define-public r-dose (package (name "r-dose") - (version "3.22.0") + (version "3.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp")))) + "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 83f0c1a39d60048e00691205ad42b4a0ab5efc70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:55 +0200 Subject: gnu: r-enrichplot: Update to 1.16.2. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f606439884..61aa7eac49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9385,14 +9385,14 @@ (define-public r-dose (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02")))) + "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss")))) (build-system r-build-system) (propagated-inputs (list r-aplot -- cgit v1.2.3 From 597106f23444b799e30e6a1d183ec4e541ad97e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:55 +0200 Subject: gnu: r-rgadem: Update to 2.44.1. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61aa7eac49..950796458b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9807,14 +9807,14 @@ (define-public r-bacon (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.0") + (version "2.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4")))) + "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 23e42e77d43d245044d34b809e11fa275e8f71e8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:55 +0200 Subject: gnu: r-rsubread: Update to 2.10.5. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 950796458b..2c1d2e5883 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11502,14 +11502,14 @@ (define-public r-annotatr (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.4") + (version "2.10.5") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl")))) + "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 1c3750c9eacc8b2ca3872551150579549d895a5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:55 +0200 Subject: gnu: r-ncdfflow: Update to 2.42.1. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c1d2e5883..2926e4cbb8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11704,14 +11704,14 @@ (define-public r-flowmeans (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m")))) + "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f82d20caaee86d8c8fd91e07181264fce398b70a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:56 +0200 Subject: gnu: r-ggcyto: Update to 1.24.1. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2926e4cbb8..bbbe7e9fa4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11735,14 +11735,14 @@ (define-public r-ncdfflow (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359")))) + "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eed76ad91a4ccdd183c856263f079ca625c46551 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:56 +0200 Subject: gnu: r-flowviz: Update to 1.60.2. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.60.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bbbe7e9fa4..6a589f46eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11772,14 +11772,14 @@ (define-public r-ggcyto (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.0") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f")))) + "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bceed10243ef9c11010d6d1fffaa79afe4954542 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:56 +0200 Subject: gnu: r-flowstats: Update to 4.8.2. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.8.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a589f46eb..150d816933 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11920,14 +11920,14 @@ (define-public r-flowworkspace (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.0") + (version "4.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) + "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 10c006c21d42d78b6b0dbe4e1ef602a31fc829e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:56 +0200 Subject: gnu: r-opencyto: Update to 2.8.4. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.8.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 150d816933..59f4c35a9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11958,14 +11958,14 @@ (define-public r-flowstats (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.0") + (version "2.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) + "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e30b2aeaa213601e7743e7b4d8fb88b8ed98e883 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:56 +0200 Subject: gnu: r-cytoml: Update to 2.8.1. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59f4c35a9e..09c3b9b3bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12002,14 +12002,14 @@ (define-public r-opencyto (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr")))) + "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 8441c1f9ea19aab1a69290e2a9b7b0a13808e999 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:57 +0200 Subject: gnu: r-bioccheck: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.32.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09c3b9b3bb..cb0bcbd893 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13761,13 +13761,13 @@ (define-public r-bioccasestudies (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc")))) + "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From 9af834ad37af4acfa451177f3b4d5e4a5063756a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:57 +0200 Subject: gnu: r-biocviews: Update to 1.64.1. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.64.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb0bcbd893..fbc4a679fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13836,13 +13836,13 @@ (define-public r-biocstyle (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126")))) + "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 78ff15ae42266465bdf3cff2a0ec052563d07095 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:57 +0200 Subject: gnu: r-biocpkgtools: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbc4a679fd..3311154b72 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14032,14 +14032,14 @@ (define-public r-biocor (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h")))) + "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d66a4669091e592af7670e0521517131e6f82f10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-hdf5array: Update to 1.24.2. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.24.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3311154b72..a3cfe16d17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14578,14 +14578,14 @@ (define-public r-hitc (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.1") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday")))) + "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 1527d2e9df7ddd83df5d2f40deaf549878cf22ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-scuttle: Update to 1.6.3. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.6.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3cfe16d17..5ccf327c21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14979,14 +14979,14 @@ (define-public r-singler (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn")))) + "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cc719399c98f133a951977867974e2bce9b854be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-scran: Update to 1.24.1. * gnu/packages/bioconductor.scm (r-scran): Update to 1.24.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ccf327c21..56640caed1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15056,14 +15056,14 @@ (define-public r-scater (define-public r-scran (package (name "r-scran") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w")))) + "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni")))) (build-system r-build-system) (propagated-inputs (list r-beachmat -- cgit v1.2.3 From 547d4670e73fefb92c2728f07d02ce76e9491690 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-delayedmatrixstats: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56640caed1..c5e94a60ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15124,14 +15124,14 @@ (define-public r-sparsematrixstats (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv")))) + "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From 869b1f9f5c4ce4390b0d560809a8939ee6b87500 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-pathview: Update to 1.36.1. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c5e94a60ba..cb6d39cac0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15806,13 +15806,13 @@ (define-public r-spp (define-public r-pathview (package (name "r-pathview") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq")))) + (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2e7872f6c928d94ac9b35556d6c43171c0b32fba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:58 +0200 Subject: gnu: r-bgeecall: Update to 1.12.2. * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.12.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb6d39cac0..74dd1ecd6c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16055,14 +16055,14 @@ (define-public r-beclear (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh")))) + "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6bf59194a64f89ed8acb292ddcb501bcf0f140e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:59 +0200 Subject: gnu: r-basilisk: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-basilisk): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74dd1ecd6c..e4cf665f05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16244,14 +16244,14 @@ (define-public r-basilisk-utils (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh")))) + "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 87c097631fa6ae6dcc6019d1aefd585c52358d69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:59 +0200 Subject: gnu: r-biocdockermanager: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4cf665f05..c25cf53d31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16304,14 +16304,14 @@ (define-public r-biocthis (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6")))) + "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) -- cgit v1.2.3 From 202fd44ca08054f9aa9527c9ba1fb8777a5ddcad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:59 +0200 Subject: gnu: r-biodb: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c25cf53d31..cc4b34a2ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16334,14 +16334,14 @@ (define-public r-biocdockermanager (define-public r-biodb (package (name "r-biodb") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni")))) + "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 94693d1980f9b8f65a61c601d130f1265d362124 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:59 +0200 Subject: gnu: r-bionero: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-bionero): Update to 1.4.2. [propagated-inputs]: Remove r-deseq2 and r-ggpubr; add r-ggrepel and r-patchwork. --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cc4b34a2ca..4e732347fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16475,32 +16475,32 @@ (define-public r-biomvrcns (define-public r-bionero (package (name "r-bionero") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj")))) + "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-complexheatmap - r-deseq2 r-dynamictreecut r-genie3 r-ggnetwork r-ggnewscale r-ggplot2 - r-ggpubr + r-ggrepel r-igraph r-intergraph r-matrixstats r-minet r-netrep r-networkd3 + r-patchwork r-rcolorbrewer r-reshape2 r-summarizedexperiment -- cgit v1.2.3 From 17134b9ec1aad94d41d75217a919dd1b224549d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 3 Oct 2022 18:20:59 +0200 Subject: gnu: r-tximeta: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e732347fe..0a491f3d00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17010,14 +17010,14 @@ (define-public r-tricycle (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl")))) + "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e069c6df5e2685bceba6dc27f4f8eab35894ce6c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 6 Oct 2022 12:38:34 +0200 Subject: gnu: Add r-dada2. * gnu/packages/bioconductor.scm (r-dada2): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a491f3d00..ecb60f2e24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16743,6 +16743,43 @@ (define-public r-bsseq visualizing bisulfite sequencing data.") (license license:artistic2.0))) +(define-public r-dada2 + (package + (name "r-dada2") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dada2" version)) + (sha256 + (base32 + "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + (properties `((upstream-name . "dada2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppparallel + r-reshape2 + r-shortread + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://benjjneb.github.io/dada2/") + (synopsis + "Accurate, high-resolution sample inference from amplicon sequencing data") + (description + "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs) +from high-throughput amplicon sequencing data, replacing the coarser and less +accurate OTU clustering approach. The dada2 pipeline takes as input +demultiplexed fastq files, and outputs the sequence variants and their +sample-wise abundances after removing substitution and chimera errors. +Taxonomic classification is available via a native implementation of the RDP +naive Bayesian classifier, and species-level assignment to 16S rRNA gene +fragments by exact matching.") + (license license:lgpl2.0))) + (define-public r-dmrseq (package (name "r-dmrseq") -- cgit v1.2.3 From 5d58d2068423e2358044737fc27e5c4b875a5d20 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 14 Oct 2022 19:27:28 +0200 Subject: gnu: Add r-macrophage. X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioconductor.scm (r-macrophage): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecb60f2e24..3692bb94af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1384,6 +1384,29 @@ (define-public r-genomationdata downloaded from Encode.") (license license:gpl3+))) +(define-public r-macrophage + (package + (name "r-macrophage") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "macrophage" version + 'experiment)) + (sha256 + (base32 + "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms")))) + (properties `((upstream-name . "macrophage"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/macrophage") + (synopsis "Human macrophage immune response data") + (description + "This package provides the output of running @code{Salmon} on a set of 24 +RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and +gene expression indicate a role for enhancer priming in immune response\", published +in Nature Genetics, January 2018.") + (license license:gpl2+))) + (define-public r-msdata (package (name "r-msdata") -- cgit v1.2.3 From 4b9fa56cadf7442addf22451fc4a7d5a0d34879e Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 27 Oct 2022 00:38:09 +0200 Subject: gnu: Add r-baalchip. * gnu/packages/bioconductor.scm (r-baalchip): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3692bb94af..b323541f82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2293,6 +2293,46 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-baalchip + (package + (name "r-baalchip") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaalChIP" version)) + (sha256 + (base32 + "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + (properties `((upstream-name . "BaalChIP"))) + (build-system r-build-system) + (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl + (propagated-inputs + (list r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BaalChIP") + (synopsis + "Analysis of allele-specific transcription factor binding in cancer genomes") + (description + "This package offers functions to process multiple @code{ChIP-seq BAM} +files and detect allele-specific events. It computes allele counts at +individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality +control) steps to remove problematic variants, and utilizes a Bayesian +framework to identify statistically significant allele-specific events. +BaalChIP is able to account for copy number differences between the two +alleles, a known phenotypical feature of cancer samples.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From f180a5990b133790fbf7f60fb9c9ea4f8fa98f08 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 14 Oct 2022 19:01:42 +0200 Subject: gnu: Add r-fishpond. * gnu/packages/bioconductor.scm (r-fishpond): New variable. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b323541f82..65df5d1f11 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14585,6 +14585,44 @@ (define-public r-rgraphviz objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fishpond + (package + (name "r-fishpond") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "fishpond" version)) + (sha256 + (base32 + "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + (properties `((upstream-name . "fishpond"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-abind + r-genomicranges + r-gtools + r-iranges + r-jsonlite + r-matrix + r-matrixstats + r-qvalue + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-svmisc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/fishpond") + (synopsis "Downstream methods and tools for expression data") + (description + "The @code{fishpond} package contains methods for differential transcript +and gene expression analysis of RNA-seq data using inferential replicates for +uncertainty of abundance quantification, as generated by Gibbs sampling or +bootstrap sampling. Also the package contains a number of utilities for +working with Salmon and Alevin quantification files.") + (license license:gpl2))) + (define-public r-fithic (package (name "r-fithic") -- cgit v1.2.3 From 9f8ab16fb538b3f0721ab7b188e9997e8440058d Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 14 Oct 2022 13:12:16 +0200 Subject: gnu: Add r-tximportdata. * gnu/packages/bioconductor.scm (r-tximportdata): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65df5d1f11..b45da78f68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1628,6 +1628,30 @@ (define-public r-tcgabiolinksgui-data TCGAbiolinksGUI package.") (license license:gpl3))) +(define-public r-tximportdata + (package + (name "r-tximportdata") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximportData" version + 'experiment)) + (sha256 + (base32 + "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy")))) + (properties `((upstream-name . "tximportData"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tximportData") + (synopsis "Data for the tximport package") + (description + "This package provides the output of running various transcript abundance +quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The +quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon} +and @code{Sailfish}. Alevin example output is also included.") + (license license:gpl2+))) + + ;;; Packages -- cgit v1.2.3 From f31b494bb69068b5d3bdd75351c5497962e2d2fd Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 28 Jun 2022 17:13:54 +0200 Subject: gnu: Add r-basespacer. * gnu/packages/bioconductor.scm (r-basespacer): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b45da78f68..784ddbfae3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2357,6 +2357,29 @@ (define-public r-baalchip alleles, a known phenotypical feature of cancer samples.") (license license:artistic2.0))) +(define-public r-basespacer + (package + (name "r-basespacer") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaseSpaceR" version)) + (sha256 + (base32 + "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj")))) + (properties `((upstream-name . "BaseSpaceR"))) + (build-system r-build-system) + (propagated-inputs (list r-rcurl r-rjsonio)) + (home-page "https://bioconductor.org/packages/BaseSpaceR") + (synopsis "R SDK for BaseSpace RESTful API") + (description + "This package provides an R interface to Illumina's BaseSpace cloud +computing environment, enabling the fast development of data analysis and +visualization tools. Besides providing an easy to use set of tools for +manipulating the data from BaseSpace, it also facilitates the access to R's +rich environment of statistical and data analysis tools.") + (license license:asl2.0))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From 0ad89a84c3e86093b4c17fd926a04cfc0228c6da Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 27 Jun 2022 23:16:20 +0200 Subject: gnu: Add r-bac. * gnu/packages/bioconductor.scm (r-bac): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 784ddbfae3..2e13a86774 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2380,6 +2380,30 @@ (define-public r-basespacer rich environment of statistical and data analysis tools.") (license license:asl2.0))) +(define-public r-bac + (package + (name "r-bac") + (version "1.56.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BAC" version)) + (sha256 + (base32 + "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2")))) + (properties `((upstream-name . "BAC"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BAC") + (synopsis "Bayesian analysis of Chip-chip experiment") + (description + "This package uses a Bayesian hierarchical model to detect enriched +regions from ChIP-chip experiments. The common goal in analyzing this +ChIP-chip data is to detect DNA-protein interactions from ChIP-chip +experiments. The BAC package has mainly been tested with Affymetrix tiling +array data. However, we expect it to work with other platforms (e.g. Agilent, +Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so +you will have to normalize your data beforehand.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From c969517cec2b403c13cb9150e12a4e6804b5326e Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 27 Jun 2022 23:28:24 +0200 Subject: gnu: Add r-bader. * gnu/packages/bioconductor.scm (r-bader): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e13a86774..111785800f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2404,6 +2404,30 @@ (define-public r-bac you will have to normalize your data beforehand.") (license license:artistic2.0))) +(define-public r-bader + (package + (name "r-bader") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BADER" version)) + (sha256 + (base32 + "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm")))) + (properties `((upstream-name . "BADER"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BADER") + (synopsis + "Bayesian analysis of differential expression in RNA sequencing data") + (description + "The BADER package is intended for the analysis of RNA sequencing data. +The algorithm fits a Bayesian hierarchical model for RNA sequencing count +data. BADER returns the posterior probability of differential expression for +each gene between two groups A and B. The joint posterior distribution of the +variables in the model can be returned in the form of posterior samples, which +can be used for further down-stream analyses such as gene set enrichment.") + (license license:gpl2))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From f0d0b6a0c5e3cc5d7232ef16c5ded3dfc458bf01 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 27 Jun 2022 23:39:36 +0200 Subject: gnu: Add r-badregionfinder. * gnu/packages/bioconductor.scm (r-badregionfinder): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 111785800f..7aef32286a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2428,6 +2428,33 @@ (define-public r-bader can be used for further down-stream analyses such as gene set enrichment.") (license license:gpl2))) +(define-public r-badregionfinder + (package + (name "r-badregionfinder") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BadRegionFinder" version)) + (sha256 + (base32 + "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9")))) + (properties `((upstream-name . "BadRegionFinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomart + r-genomicranges + r-rsamtools + r-s4vectors + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BadRegionFinder") + (synopsis "Identifying regions with bad coverage in sequence alignment data") + (description + "BadRegionFinder is a package for identifying regions with a bad, +acceptable and good coverage in sequence alignment data available as bam +files. The whole genome may be considered as well as a set of target regions. +Various visual and textual types of output are available.") + (license license:lgpl3))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From 9b337c2735f522a8fcaa1e7972df4a76f97d29b8 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 28 Jun 2022 00:17:52 +0200 Subject: gnu: Add r-bambu. * gnu/packages/bioconductor.scm (r-bambu): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7aef32286a..3a53ebdf95 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2455,6 +2455,49 @@ (define-public r-badregionfinder Various visual and textual types of output are available.") (license license:lgpl3))) +(define-public r-bambu + (package + (name "r-bambu") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bambu" version)) + (sha256 + (base32 + "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w")))) + (properties `((upstream-name . "bambu"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-bsgenome + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tidyr + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/GoekeLab/bambu") + (synopsis + "Isoform reconstruction and quantification for long read RNA-Seq data") + (description + "This R package is for multi-sample transcript discovery and +quantification using long read RNA-Seq data. You can use bambu after read +alignment to obtain expression estimates for known and novel transcripts and +genes. The output from bambu can directly be used for visualisation and +downstream analysis, such as differential gene expression or transcript +usage.") + (license license:gpl3))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From fe2be9c0cf4d4327f8ef9eda1668de76cbc4fca7 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 28 Jun 2022 00:34:03 +0200 Subject: gnu: Add r-bandits. * gnu/packages/bioconductor.scm (r-bandits): New variable. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a53ebdf95..c8a15c5123 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2498,6 +2498,44 @@ (define-public r-bambu usage.") (license license:gpl3))) +(define-public r-bandits + (package + (name "r-bandits") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BANDITS" version)) + (sha256 + (base32 + "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9")))) + (properties `((upstream-name . "BANDITS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-doparallel + r-dorng + r-drimseq + r-foreach + r-ggplot2 + r-mass + r-r-utils + r-rcpp + r-rcpparmadillo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SimoneTiberi/BANDITS") + (synopsis "Bayesian analysis of differential splicing") + (description + "BANDITS is a Bayesian hierarchical model for detecting differential +splicing of genes and transcripts, via @dfn{DTU} (differential transcript +usage), between two or more conditions. The method uses a Bayesian +hierarchical framework, which allows for sample specific proportions in a +Dirichlet-Multinomial model, and samples the allocation of fragments to the +transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte +Carlo) techniques and a DTU test is performed via a multivariate Wald test on +the posterior densities for the average relative abundance of transcripts.") + (license license:gpl3+))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From 01944e0eb8a988a4ff26b93e95b3c04ca6935b14 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 28 Jun 2022 00:42:13 +0200 Subject: gnu: Add r-banocc. * gnu/packages/bioconductor.scm (r-banocc): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8a15c5123..c7d759d15b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2536,6 +2536,34 @@ (define-public r-bandits the posterior densities for the average relative abundance of transcripts.") (license license:gpl3+))) +(define-public r-banocc + (package + (name "r-banocc") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "banocc" version)) + (sha256 + (base32 + "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx")))) + (properties `((upstream-name . "banocc"))) + (build-system r-build-system) + (propagated-inputs + (list r-coda + r-mvtnorm + r-rstan + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/banocc") + (synopsis "Bayesian analysis of compositional covariance") + (description + "BAnOCC is a package designed for compositional data, where each sample +sums to one. It infers the approximate covariance of the unconstrained data +using a Bayesian model coded with @code{rstan}. It provides as output the +@code{stanfit} object as well as posterior median and credible interval +estimates for each correlation element.") + (license license:expat))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From 38cc09493c59da72b2858a3ee0bd5443b5e7af52 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 28 Jun 2022 17:00:44 +0200 Subject: gnu: Add r-barcodetrackr. * gnu/packages/bioconductor.scm (r-barcodetrackr): New variable. --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7d759d15b..65f4debbac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2564,6 +2564,48 @@ (define-public r-banocc estimates for each correlation element.") (license license:expat))) +(define-public r-barcodetrackr + (package + (name "r-barcodetrackr") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "barcodetrackR" version)) + (sha256 + (base32 + "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3")))) + (properties `((upstream-name . "barcodetrackR"))) + (build-system r-build-system) + (propagated-inputs + (list r-circlize + r-cowplot + r-dplyr + r-ggdendro + r-ggplot2 + r-ggridges + r-magrittr + r-plyr + r-proxy + r-rcolorbrewer + r-rlang + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/dunbarlabNIH/barcodetrackR") + (synopsis "Functions for analyzing cellular barcoding data") + (description + "This package is developed for the analysis and visualization of clonal +tracking data. The required data is formed by samples and tag abundances in +matrix form, usually from cellular barcoding experiments, integration site +retrieval analyses, or similar technologies.") + (license license:cc0))) + (define-public r-biocversion (package (name "r-biocversion") -- cgit v1.2.3 From 930b1e04585fe0ecd8c8792093ebc8ebb509ad4b Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 14:44:54 +0200 Subject: gnu: Add r-awst. * gnu/packages/bioconductor.scm (r-awst): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65f4debbac..f048caa9fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,33 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-awst + (package + (name "r-awst") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "awst" version)) + (sha256 + (base32 + "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav")))) + (properties `((upstream-name . "awst"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/drisso/awst") + (synopsis "Asymmetric within-sample transformation") + (description + "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that +regularizes RNA-seq read counts and reduces the effect of noise on the +classification of samples. AWST comprises two main steps: standardization and +smoothing. These steps transform gene expression data to reduce the noise of +the lowly expressed features, which suffer from background effects and low +signal-to-noise ratio, and the influence of the highly expressed features, +which may be the result of amplification bias and other experimental +artifacts.") + (license license:expat))) + (define-public r-baalchip (package (name "r-baalchip") -- cgit v1.2.3 From 3f755098cb6d92d5bbe9e4f780ec1d5a5c74e9b5 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 14:26:29 +0200 Subject: gnu: Add r-awfisher. * gnu/packages/bioconductor.scm (r-awfisher): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f048caa9fb..e7354aa4e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,30 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-awfisher + (package + (name "r-awfisher") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AWFisher" version)) + (sha256 + (base32 + "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1")))) + (properties `((upstream-name . "AWFisher"))) + (build-system r-build-system) + (propagated-inputs + (list r-edger + r-limma)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AWFisher") + (synopsis "Fast computing for adaptively weighted fisher's method") + (description + "This package is an implementation of the Adaptively Weighted Fisher's +method, including fast p-value computing, variability index, and +meta-pattern.") + (license license:gpl3))) + (define-public r-awst (package (name "r-awst") -- cgit v1.2.3 From 599655dc496491c2569689811d667df6ffeb396c Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 13:54:42 +0200 Subject: gnu: Add r-attract. * gnu/packages/bioconductor.scm (r-attract): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7354aa4e3..ad20602ff6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,37 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-attract + (package + (name "r-attract") + (version "1.48.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "attract" version)) + (sha256 + (base32 + "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82")))) + (properties `((upstream-name . "attract"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biobase + r-cluster + r-gostats + r-keggrest + r-limma + r-org-hs-eg-db + r-reactome-db)) + (home-page "https://bioconductor.org/packages/attract") + (synopsis "Finding drivers of Kauffman's attractor landscape") + (description + "This package contains the functions to find the gene expression modules +that represent the drivers of Kauffman's attractor landscape. The modules are +the core attractor pathways that discriminate between different cell types of +groups of interest. Each pathway has a set of synexpression groups, which show +transcriptionally-coordinated changes in gene expression.") + (license license:lgpl2.0+))) + (define-public r-awfisher (package (name "r-awfisher") -- cgit v1.2.3 From 70d30096b38f4d1d23d84aaae34400e3d8abd797 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 12:46:31 +0200 Subject: gnu: Add r-atsnp. * gnu/packages/bioconductor.scm (r-atsnp): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad20602ff6..6e72a8e1af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,39 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-atsnp + (package + (name "r-atsnp") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atSNP" version)) + (sha256 + (base32 + "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz")))) + (properties `((upstream-name . "atSNP"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocfilecache + r-biocparallel + r-bsgenome + r-data-table + r-ggplot2 + r-lifecycle + r-motifstack + r-rappdirs + r-rcpp + r-testthat)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sunyoungshin/atSNP") + (synopsis + "Affinity test for identifying regulatory single nucleotide polymorphisms") + (description + "The atSNP package performs affinity tests of motif matches with the +@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and +SNP-led changes in motif matches.") + (license license:gpl2))) + (define-public r-attract (package (name "r-attract") -- cgit v1.2.3 From c0278aa51e08bc5c9916f2b58b7b45676863844f Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 12:25:20 +0200 Subject: gnu: Add r-atena. * gnu/packages/bioconductor.scm (r-atena): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6e72a8e1af..038532c915 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,47 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-atena + (package + (name "r-atena") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atena" version)) + (sha256 + (base32 + "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp")))) + (properties `((upstream-name . "atena"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-s4vectors + r-scales + r-sparsematrixstats + r-squarem + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/functionalgenomics/atena") + (synopsis "Analysis of transposable elements") + (description + "The atena package quantifies expression of @dfn{TEs} (transposable +elements) from RNA-seq data through different methods, including ERVmap, +TEtranscripts and Telescope. A common interface is provided to use each of +these methods, which consists of building a parameter object, calling the +quantification function with this object and getting a +@code{SummarizedExperiment} object as an output container of the quantified +expression profiles. The implementation allows quantifing TEs and gene +transcripts in an integrated manner.") + (license license:artistic2.0))) + (define-public r-atsnp (package (name "r-atsnp") -- cgit v1.2.3 From f1750236c139a5015631db0f4b70a4d8b7d76b5b Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 12:02:44 +0200 Subject: gnu: Add r-asset. * gnu/packages/bioconductor.scm (r-asset): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 038532c915..a0ecec8498 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,33 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-asset + (package + (name "r-asset") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASSET" version)) + (sha256 + (base32 + "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg")))) + (properties `((upstream-name . "ASSET"))) + (build-system r-build-system) + (propagated-inputs (list r-mass r-msm r-rmeta)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASSET") + (synopsis + "Subset-based association analysis of heterogeneous traits and subtypes") + (description + "This package is an R program for the subset-based analysis of +heterogeneous traits and disease subtypes. ASSET allows the user to search +through all possible subsets of z-scores to identify the subset of traits +giving the best meta-analyzed z-score. Further, it returns a p-value +adjusting for the multiple-testing involved in the search. It also allows for +searching for the best combination of disease subtypes associated with each +variant.") + (license license:gpl2))) + (define-public r-atena (package (name "r-atena") -- cgit v1.2.3 From a8e0069f87d65185bd426041373051de80057414 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 23 Jun 2022 11:42:57 +0200 Subject: gnu: Add r-assessorf. * gnu/packages/bioconductor.scm (r-assessorf): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0ecec8498..67a62faa46 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,35 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-assessorf + (package + (name "r-assessorf") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AssessORF" version)) + (sha256 + (base32 + "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7")))) + (properties `((upstream-name . "AssessORF"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-decipher + r-genomicranges + r-iranges)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AssessORF") + (synopsis "Assess gene predictions using proteomics and evolutionary conservation") + (description + "In order to assess the quality of a set of predicted genes for a genome, +evidence must first be mapped to that genome. Next, each gene must be +categorized based on how strong the evidence is for or against that gene. The +AssessORF package provides the functions and class structures necessary for +accomplishing those tasks, using proteomics hits and evolutionarily conserved +start codons as the forms of evidence.") + (license license:gpl3))) + (define-public r-asset (package (name "r-asset") -- cgit v1.2.3 From b8b91756abe83c416fd38e55cf8cf52f6d681be5 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 22 Jun 2022 16:46:12 +0200 Subject: gnu: Add r-aspli. * gnu/packages/bioconductor.scm (r-aspli): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67a62faa46..375104648b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,54 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-aspli + (package + (name "r-aspli") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASpli" version)) + (sha256 + (base32 + "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz")))) + (properties `((upstream-name . "ASpli"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocstyle + r-data-table + r-dt + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gviz + r-htmltools + r-igraph + r-iranges + r-limma + r-mass + r-pbmcapply + r-rsamtools + r-s4vectors + r-tidyr + r-upsetr)) + (home-page "https://bioconductor.org/packages/ASpli") + (synopsis "Analysis of alternative splicing using RNA-Seq") + (description + "@dfn{AS} (alternative splicing) is a common mechanism of +post-transcriptional gene regulation in eukaryotic organisms that expands the +functional and regulatory diversity of a single gene by generating multiple +mRNA isoforms that encode structurally and functionally distinct proteins. +ASpli is an integrative pipeline and user-friendly R package that facilitates +the analysis of changes in both annotated and novel AS events. ASpli +integrates several independent signals in order to deal with the complexity +that might arise in splicing patterns.") + ;; The authors didn't specify any GPL version in description or in the + ;; sources. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-assessorf (package (name "r-assessorf") -- cgit v1.2.3 From 695d7720efbe72f03227a84ce557eb1a4f37d4fa Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 22 Jun 2022 16:07:05 +0200 Subject: gnu: Add r-asgsca. * gnu/packages/bioconductor.scm (r-asgsca): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 375104648b..2ace372c58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,29 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-asgsca + (package + (name "r-asgsca") + (version "1.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASGSCA" version)) + (sha256 + (base32 + "0mxrrkm2lg7gxjh8ynn6qmryn8wqda7b83sr51dpgblay83jcbaq")))) + (properties `((upstream-name . "ASGSCA"))) + (build-system r-build-system) + (propagated-inputs (list r-mass r-matrix)) + (home-page "https://bioconductor.org/packages/ASGSCA") + (synopsis "Analysis of associations between multiple genotypes and traits") + (description + "The package @dfn{ASGSCA} (Association Study using Generalized Structured +Component Analysis) provides tools to model and test the association between +multiple genotypes and multiple traits, taking into account the prior +biological knowledge. Genes, and clinical pathways are incorporated in the +model as latent variables.") + (license license:gpl3))) + (define-public r-aspli (package (name "r-aspli") -- cgit v1.2.3 From aef2425666b47f5b9df24db2e0193e582d0782a5 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 22 Jun 2022 15:57:41 +0200 Subject: gnu: Add r-aseb. * gnu/packages/bioconductor.scm (r-aseb): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ace372c58..b8535250f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2317,6 +2317,33 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-aseb + (package + (name "r-aseb") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASEB" version)) + (sha256 + (base32 + "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + (properties `((upstream-name . "ASEB"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/ASEB") + (synopsis "Predict acetylated lysine sites") + (description + "ASEB is an R package to predict lysine sites that can be acetylated by a +specific @dfn{KAT} (K-acetyl-transferases) family. Lysine acetylation is a +well-studied posttranslational modification on kinds of proteins. About four +thousand lysine acetylation sites and over 20 lysine KATs have been +identified. However, which KAT is responsible for a given protein or lysine +site acetylation is mostly unknown. In this package, we use a +@dfn{GSEA}-like (Gene Set Enrichment Analysis) method to make predictions. +GSEA method was developed and successfully used to detect coordinated +expression changes and find the putative functions of the long non-coding +RNAs.") + (license license:gpl3+))) + (define-public r-asgsca (package (name "r-asgsca") -- cgit v1.2.3 From 917b96cef74ba74294e1eeaf9f20d5cec1dddb7c Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 28 Oct 2022 07:02:35 +0200 Subject: gnu: Add r-debcam. * gnu/packages/bioconductor.scm (r-debcam): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8535250f9..23d7d5b3bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -48,6 +48,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -3051,6 +3052,45 @@ (define-public r-dearseq set analyses, and can deal with repeated or longitudinal data.") (license license:gpl2))) +(define-public r-debcam + (package + (name "r-debcam") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "debCAM" version)) + (sha256 + (base32 + "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + (properties `((upstream-name . "debCAM"))) + (build-system r-build-system) + (inputs (list openjdk)) + (propagated-inputs + (list r-apcluster + r-biobase + r-biocparallel + r-corpcor + r-dmwr2 + r-geometry + r-nmf + r-nnls + r-pcapp + r-rjava + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/debCAM") + (synopsis "Deconvolution by convex analysis of mixtures") + (description + "This package is an R implementation for fully unsupervised deconvolution +of complex tissues. DebCAM provides basic functions to perform unsupervised +deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis +of Mixtures} and some auxiliary functions to help understand the +subpopulation- specific results. It also implements functions to perform +supervised deconvolution based on prior knowledge of molecular markers, S +matrix or A matrix. Combining molecular markers from CAM and from prior +knowledge can achieve semi-supervised deconvolution of mixtures.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher") -- cgit v1.2.3 From 812cbd9321c8fdebf62afbc43aee106f91227072 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 28 Oct 2022 04:53:52 +0200 Subject: gnu: Add r-dama. * gnu/packages/bioconductor.scm (r-dama): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23d7d5b3bf..08eb33e4e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3014,6 +3014,28 @@ (define-public r-cummerbund used visualizations.") (license license:artistic2.0))) +(define-public r-dama + (package + (name "r-dama") + (version "1.68.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "daMA" version)) + (sha256 + (base32 + "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m")))) + (properties `((upstream-name . "daMA"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html") + (synopsis + "Efficient design and analysis of factorial two-colour microarray data") + (description + "This package contains functions for the efficient design of factorial +two-colour microarray experiments and for the statistical analysis of +factorial microarray data.") + (license license:gpl2+))) + (define-public r-dearseq (package (name "r-dearseq") -- cgit v1.2.3 From fe20121dc7b19d1804acc086707fa0c9463d3127 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 28 Oct 2022 04:53:53 +0200 Subject: gnu: Add r-damefinder. * gnu/packages/bioconductor.scm (r-damefinder): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08eb33e4e0..9e463457f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3036,6 +3036,47 @@ (define-public r-dama factorial microarray data.") (license license:gpl2+))) +(define-public r-damefinder + (package + (name "r-damefinder") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DAMEfinder" version)) + (sha256 + (base32 + "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf")))) + (properties `((upstream-name . "DAMEfinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bumphunter + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-plyr + r-readr + r-reshape2 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DAMEfinder") + (synopsis "Differential allelicly methylated regions") + (description + "This package offers functionality for taking methtuple or Bismark +outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and +compute @acronym{DAMEs, Differential Allelicly MEthylated} regions. It also +offers nice visualization of methyl-circle plots.") + (license license:expat))) + (define-public r-dearseq (package (name "r-dearseq") -- cgit v1.2.3 From 41461b6e22bbad937737d1a5ca4f2826d09a8463 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 30 Oct 2022 01:16:04 +0200 Subject: gnu: Add r-deco. * gnu/packages/bioconductor.scm (r-deco): New variable. --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e463457f2..e25c4d0e95 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3178,6 +3178,48 @@ (define-public r-decipher biological sequences.") (license license:gpl3))) +(define-public r-deco + (package + (name "r-deco") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deco" version)) + (sha256 + (base32 + "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m")))) + (properties `((upstream-name . "deco"))) + (build-system r-build-system) + (propagated-inputs + (list r-ade4 + r-annotationdbi + r-biobase + r-biocparallel + r-biocstyle + r-cluster + r-foreign + r-gdata + r-ggplot2 + r-gplots + r-gridextra + r-limma + r-locfit + r-made4 + r-rcolorbrewer + r-reshape2 + r-scatterplot3d + r-sfsmisc + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/fjcamlab/deco") + (synopsis "Decomposing heterogeneous cohorts using omic data profiling") + (description + "This package discovers differential features in hetero- and homogeneous +omic data by a two-step method including subsampling LIMMA and NSCA. DECO +reveals feature associations to hidden subclasses not exclusively related to +higher deregulation levels.") + (license license:gpl3+))) + (define-public r-deconvr (package (name "r-deconvr") -- cgit v1.2.3 From a8631c816d78ede76f279e288efbb284090f8c91 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 30 Oct 2022 01:16:05 +0200 Subject: gnu: Add r-decomplexdisease. * gnu/packages/bioconductor.scm (r-decomplexdisease): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e25c4d0e95..e4c8d9cdb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3220,6 +3220,39 @@ (define-public r-deco higher deregulation levels.") (license license:gpl3+))) +(define-public r-decomplexdisease + (package + (name "r-decomplexdisease") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DEComplexDisease" version)) + (sha256 + (base32 + "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d")))) + (properties `((upstream-name . "DEComplexDisease"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-edger + r-rcpp + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DEComplexDisease") + (synopsis "Investigations of complex diseases by bi-clustering analysis") + (description + "DEComplexDisease is designed to find the @acronym{DEGs, Differential +Expressed Genes} for complex disease, which is characterized by the +heterogeneous genomic expression profiles. Different from the established DEG +analysis tools, it does not assume the patients of complex diseases to share +the common DEGs. By applying a bi-clustering algorithm, DEComplexDisease +finds the DEGs shared by as many patients. Applying the DEComplexDisease +analysis results, users are possible to find the patients affected by the same +mechanism based on the shared signatures.") + (license license:gpl3))) + (define-public r-deconvr (package (name "r-deconvr") -- cgit v1.2.3 From ae94d879a1179d372e68a9fe7df14311be7b9789 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 30 Oct 2022 01:16:06 +0200 Subject: gnu: Add r-decomptumor2sig. * gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4c8d9cdb5..80acaee764 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3253,6 +3253,49 @@ (define-public r-decomplexdisease mechanism based on the shared signatures.") (license license:gpl3))) +(define-public r-decomptumor2sig + (package + (name "r-decomptumor2sig") + (version "2.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decompTumor2Sig" version)) + (sha256 + (base32 + "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + (properties `((upstream-name . "decompTumor2Sig"))) + (build-system r-build-system) + (inputs (list perl)) ;script/extractSpecColumns.pl + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-data-table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-matrix + r-plyr + r-quadprog + r-readxl + r-s4vectors + r-summarizedexperiment + r-txdb-hsapiens-ucsc-hg19-knowngene + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://rmpiro.net/decompTumor2Sig/") + (synopsis "Decomposition of individual tumors into mutational signatures") + (description + "The package uses quadratic programming for signature refitting, i.e., to +decompose the mutation catalog from an individual tumor sample into a set of +given mutational signatures (either Alexandrov-model signatures or +Shiraishi-model signatures), computing weights that reflect the contributions +of the signatures to the mutation load of the tumor.") + (license license:gpl2))) + (define-public r-deconvr (package (name "r-deconvr") -- cgit v1.2.3 From fc27bf5d7469ec019ff7866b3b728afa7c434f26 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 30 Oct 2022 01:16:07 +0200 Subject: gnu: Add r-deconrnaseq. * gnu/packages/bioconductor.scm (r-deconrnaseq): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80acaee764..321a9621f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3296,6 +3296,33 @@ (define-public r-decomptumor2sig of the signatures to the mutation load of the tumor.") (license license:gpl2))) +(define-public r-deconrnaseq + (package + (name "r-deconrnaseq") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DeconRNASeq" version)) + (sha256 + (base32 + "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6")))) + (properties `((upstream-name . "DeconRNASeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-limsolve + r-pcamethods)) + (home-page "https://bioconductor.org/packages/DeconRNASeq") + (synopsis + "Deconvolution of heterogeneous tissue samples for mRNA-Seq data") + (description + "DeconSeq is an R package for deconvolution of heterogeneous tissues +based on mRNA-Seq data. It models the expression levels from heterogeneous +cell populations in mRNA-Seq as the weighted average of expression from +different constituting cell types and predicted cell type proportions of +single expression profiles.") + (license license:gpl2))) + (define-public r-deconvr (package (name "r-deconvr") -- cgit v1.2.3 From 6e0361d035d6204ed0a70ba646cfa3c54636d4a2 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 30 Oct 2022 01:16:08 +0200 Subject: gnu: Add r-decontam. * gnu/packages/bioconductor.scm (r-decontam): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 321a9621f1..6ec177d222 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3323,6 +3323,32 @@ (define-public r-deconrnaseq single expression profiles.") (license license:gpl2))) +(define-public r-decontam + (package + (name "r-decontam") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decontam" version)) + (sha256 + (base32 + "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9")))) + (properties `((upstream-name . "decontam"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/benjjneb/decontam") + (synopsis + "Identification of contaminants in marker-gene and metagenomics data") + (description + "This package offers simple statistical identification of contaminating +sequence features in marker-gene or metagenomics data. It works on any kind +of feature derived from environmental sequencing data (e.g. ASVs, OTUs, +taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced +negative control samples.") + (license license:artistic2.0))) + (define-public r-deconvr (package (name "r-deconvr") -- cgit v1.2.3 From 49b696cb588bfc1e7b1eaaeed7e819d0666b7862 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 3 May 2022 08:53:11 +0200 Subject: gnu: Add r-airpart. * gnu/packages/bioconductor.scm (r-airpart): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6ec177d222..7ece87aa7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2082,6 +2082,53 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-airpart + (package + (name "r-airpart") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "airpart" version)) + (sha256 + (base32 + "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06")))) + (properties `((upstream-name . "airpart"))) + (build-system r-build-system) + (propagated-inputs + (list r-apeglm + r-clue + r-complexheatmap + r-dplyr + r-dynamictreecut + r-emdbook + r-forestplot + r-ggplot2 + r-lpsolve + r-matrixstats + r-mclust + r-pbapply + r-plyr + r-rcolorbrewer + r-rlang + r-s4vectors + r-scater + r-singlecellexperiment + r-smurf + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/airpart") + (synopsis "Differential cell-type-specific allelic imbalance") + (description + "The airpart package identifies sets of genes displaying differential +cell-type-specific allelic imbalance across cell types or states, utilizing +single-cell allelic counts. It makes use of a generalized fused lasso with +binomial observations of allelic counts to partition cell types by their +allelic imbalance. Alternatively, a nonparametric method for partitioning +cell types is offered. The package includes a number of visualizations and +quality control functions for examining single cell allelic imbalance +datasets.") + (license license:gpl2))) + (define-public r-amountain (package (name "r-amountain") -- cgit v1.2.3 From 34b78bce57ca9806b272d4a246675cf09d94f28f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Nov 2022 08:23:01 +0100 Subject: gnu: r-valr: Update to 0.6.6. * gnu/packages/bioconductor.scm (r-valr): Update to 0.6.6. [propagated-inputs]: Add r-cli. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7ece87aa7f..8dd499403c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7281,17 +7281,18 @@ (define-public r-tximport (define-public r-valr (package (name "r-valr") - (version "0.6.5") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw")))) + "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph")))) (build-system r-build-system) (propagated-inputs (list r-broom + r-cli r-dplyr r-ggplot2 r-rcpp -- cgit v1.2.3 From 12b83f697def2679a8f8bc0d6b11690bcce48e25 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 16 Jun 2022 17:57:21 +0200 Subject: gnu: Add r-aldex2. * gnu/packages/bioconductor.scm (r-aldex2): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8dd499403c..cb9feda347 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2235,6 +2235,47 @@ (define-public r-anaquin analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) +(define-public r-aldex2 + (package + (name "r-aldex2") + (version "1.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ALDEx2" version)) + (sha256 + (base32 + "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + (properties `((upstream-name . "ALDEx2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ggloor/ALDEx_bioc") + (synopsis "Analysis of differential abundance taking sample variation into account") + (description + "This package provides a differential abundance analysis for the +comparison of two or more conditions. Useful for analyzing data from standard +RNA-seq or meta-RNA-seq assays as well as selected and unselected values from +in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer +abundance from counts, optimized for three or more experimental replicates. +The method infers biological and sampling variation to calculate the expected +false discovery rate, given the variation, based on a Wilcoxon Rank Sum test +and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a +correlation test. All tests report p-values and Benjamini-Hochberg corrected +p-values. ALDEx2 also calculates expected standardized effect sizes for +paired or unpaired study designs.") + ;; The code for the function "rdirichlet" is from the R package + ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the + ;; package's LICENSE is specified as GPL-3. + (license (list license:agpl3+ license:gpl2+ license:gpl3)))) + (define-public r-aneufinder (package (name "r-aneufinder") -- cgit v1.2.3 From 04f8295f6f91d8a5c75a212fc4b0a5174d89b996 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 19 Jun 2022 22:42:00 +0200 Subject: gnu: Add r-microbiome. * gnu/packages/bioconductor.scm (r-microbiome): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb9feda347..f3b67fd2bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9736,6 +9736,43 @@ (define-public r-bumphunter studies.") (license license:artistic2.0))) +(define-public r-microbiome + (package + (name "r-microbiome") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "microbiome" version)) + (sha256 + (base32 + "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12")))) + (properties `((upstream-name . "microbiome"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-compositions + r-dplyr + r-ggplot2 + r-phyloseq + r-reshape2 + r-rtsne + r-scales + r-tibble + r-tidyr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://microbiome.github.io/microbiome/") + (synopsis "Tools for microbiome analysis") + (description + "This package facilitates phyloseq exploration and analysis of taxonomic +profiling data. This package provides tools for the manipulation, statistical +analysis, and visualization of taxonomic profiling data. In addition to +targeted case-control studies, microbiome facilitates scalable exploration of +population cohorts. This package supports the independent phyloseq data +format and expands the available toolkit in order to facilitate the +standardization of the analyses and the development of best practices.") + (license license:bsd-2))) + (define-public r-milor (package (name "r-milor") -- cgit v1.2.3 From 093bf20cdc54add190b1184f548cb5d3a97c6ad1 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 16 Jun 2022 19:00:48 +0200 Subject: gnu: Add r-alpine. * gnu/packages/bioconductor.scm (r-alpine): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3b67fd2bf..45a511cf13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2276,6 +2276,47 @@ (define-public r-aldex2 ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript +abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million +mapped reads). It is currently designed for un-stranded paired-end RNA-seq +data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") -- cgit v1.2.3 From 8105b3c09fac897ff2c2464479b1d3e8169d8700 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 16 Nov 2022 23:21:40 +0100 Subject: gnu: Add r-hdo-db. * gnu/packages/bioconductor.scm (r-hdo-db): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45a511cf13..e55d9e357e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -506,6 +506,31 @@ (define-public r-go-db information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) +(define-public r-hdo-db + (package + (name "r-hdo-db") + (version "0.99.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDO.db" version 'annotation)) + (sha256 + (base32 + "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61")))) + (properties `((upstream-name . "HDO.db"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi)) + (native-inputs + (list r-knitr)) + (home-page "https://bioconductor.org/packages/HDO.db") + (synopsis "Annotation maps describing the entire Human Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Human Disease Ontology. The annotation data comes from +@url{Humam Disease Ontology repository, +https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") -- cgit v1.2.3 From 3d073b86d3e6bccf1f25d12174a0b88b5db65f23 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 00:38:24 +0100 Subject: gnu: Add r-biocbaseutils. * gnu/packages/bioconductor.scm (r-biocbaseutils): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e55d9e357e..0b11b5b5e9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14848,6 +14848,28 @@ (define-public r-ebarrays microarray data.") (license license:gpl2+))) +(define-public r-biocbaseutils + (package + (name "r-biocbaseutils") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocBaseUtils" version)) + (sha256 + (base32 + "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69")))) + (properties `((upstream-name . "BiocBaseUtils"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BiocBaseUtils") + (synopsis "General utility functions for developing Bioconductor packages") + (description + "The package provides utility functions related to package development. +These include functions that replace slots, and selectors for show methods. +It aims to coalesce the various helper functions often re-used throughout the +Bioconductor ecosystem.") + (license license:artistic2.0))) + (define-public r-bioccasestudies (package (name "r-bioccasestudies") -- cgit v1.2.3 From 349804b6028b471835cbdd87f4277002ca0930fc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: gnu: r-abarray: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-abarray): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b11b5b5e9..ae8dda2c05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1684,13 +1684,13 @@ (define-public r-tximportdata (define-public r-abarray (package (name "r-abarray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) + "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) -- cgit v1.2.3 From f24085bfb389e48dbed7437888a2597e65571aba Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: gnu: r-absseq: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-absseq): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae8dda2c05..7d1e8beb3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1710,13 +1710,13 @@ (define-public r-abarray (define-public r-absseq (package (name "r-absseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) + "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) -- cgit v1.2.3 From 38fc0acf4d6752a8a3dcdab41eff1b0b5ed5e2d8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: gnu: r-adam: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adam): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d1e8beb3f..acd48456f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1739,13 +1739,13 @@ (define-public r-absseq (define-public r-adam (package (name "r-adam") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) + "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr -- cgit v1.2.3 From a62284ad13b139436b2072e53e725e144782d74e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: gnu: r-adamgui: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adamgui): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index acd48456f4..a8ec425b7a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1774,13 +1774,13 @@ (define-public r-adam (define-public r-adamgui (package (name "r-adamgui") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) + "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From daf0729533c791d06cd0d3f001fb5df03eacb433 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-adimpute: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-adimpute): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8ec425b7a..526ca047c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1822,13 +1822,13 @@ (define-public r-adamgui (define-public r-adimpute (package (name "r-adimpute") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) + "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b772bc7f757d6f2c18e4e69f0f2327e5fdb36676 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-adsplit: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-adsplit): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 526ca047c1..3fd7c1aa81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1871,13 +1871,13 @@ (define-public r-adimpute (define-public r-adsplit (package (name "r-adsplit") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) + "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 69ecae7801cf12fb42300eb54e5aec655c0f85e7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-affixcan: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-affixcan): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3fd7c1aa81..f23a7775e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1899,13 +1899,13 @@ (define-public r-adsplit (define-public r-affixcan (package (name "r-affixcan") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) + "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 014fc145f8adc1d3b30be38beb88b632bc41d1fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-affyrnadegradation: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f23a7775e5..7d22e5949a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1927,13 +1927,13 @@ (define-public r-affixcan (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) + "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) -- cgit v1.2.3 From f74c670c7f21d77d1811b7f56d6b79851028f520 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-agdex: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-agdex): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d22e5949a..80b71f3c3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1952,13 +1952,13 @@ (define-public r-affyrnadegradation (define-public r-agdex (package (name "r-agdex") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) + "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) -- cgit v1.2.3 From fc60b9dfe7cd2638893fcd221009c3e991c2af42 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-aggregatebiovar: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80b71f3c3e..c753b76142 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1979,13 +1979,13 @@ (define-public r-agdex (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) + "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e153f4904d4572ab739c7b8d88e3e12c421cc542 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-agilp: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-agilp): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c753b76142..f020c608cc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2013,13 +2013,13 @@ (define-public r-aggregatebiovar (define-public r-agilp (package (name "r-agilp") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) + "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") -- cgit v1.2.3 From 5d09a99174227f4025484644ff1c89734a255d28 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-adductomicsr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f020c608cc..665f70dc48 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2035,13 +2035,13 @@ (define-public r-agilp (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) + "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fb7a1b340b3d51881241d7a3d808a7db5d509de1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-agimicrorna: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 665f70dc48..8cfcaa4074 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2080,13 +2080,13 @@ (define-public r-adductomicsr (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) + "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f217ff646354eae1f2573baec0b244350950932c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-airpart: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-airpart): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8cfcaa4074..b6769d9cac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2110,13 +2110,13 @@ (define-public r-agimicrorna (define-public r-airpart (package (name "r-airpart") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06")))) + "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c9c4d6b5017dedd33daca72e6d196b6c1dfda796 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-amountain: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-amountain): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6769d9cac..5dc75591a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2157,13 +2157,13 @@ (define-public r-airpart (define-public r-amountain (package (name "r-amountain") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) + "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) -- cgit v1.2.3 From ecb91b340469f1ad043446f5a7e94e1aebd83879 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-amaretto: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-amaretto): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5dc75591a2..15baba0931 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2181,13 +2181,13 @@ (define-public r-amountain (define-public r-amaretto (package (name "r-amaretto") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 190ed5f1374e0508924e2c0cfa23a4b5bbcd2eec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-anaquin: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-anaquin): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15baba0931..64eaf2e5a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2233,13 +2233,13 @@ (define-public r-amaretto (define-public r-anaquin (package (name "r-anaquin") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) + "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eddbd27be5968eea6a4db20f80af4aae6e234397 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: gnu: r-aldex2: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-aldex2): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64eaf2e5a6..316a14b919 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2263,13 +2263,13 @@ (define-public r-anaquin (define-public r-aldex2 (package (name "r-aldex2") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cbeefda563248df151e4d50370ff4e0d6a8a9e00 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-aneufinder: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 316a14b919..0b3b25aa55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2345,13 +2345,13 @@ (define-public r-alpine (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) + "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From d18f8e367e0142130a95e1f5c6f25a3ff1a15dd3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-anf: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-anf): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b3b25aa55..6a08187d34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2387,13 +2387,13 @@ (define-public r-aneufinder (define-public r-anf (package (name "r-anf") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj")))) + "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bc62494bc8168516030cad21ae25f686e9c0744a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-annmap: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-annmap): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a08187d34..658234ce17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2415,13 +2415,13 @@ (define-public r-anf (define-public r-annmap (package (name "r-annmap") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1114e837a9dd10b500ba81a6270c4ee47ea39dcc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-antiprofiles: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 658234ce17..bbe49a34c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2449,13 +2449,13 @@ (define-public r-annmap (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 110f0f8483b5e770cdb4010d6393f6bfa0a9e7a2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-aseb: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-aseb): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bbe49a34c1..9d3ff84bda 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2475,13 +2475,13 @@ (define-public r-antiprofiles (define-public r-aseb (package (name "r-aseb") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") -- cgit v1.2.3 From b89305c18dece7c1e4134c9af219041d7c301ef2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-asgsca: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-asgsca): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9d3ff84bda..03d364da0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2502,13 +2502,13 @@ (define-public r-aseb (define-public r-asgsca (package (name "r-asgsca") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "0mxrrkm2lg7gxjh8ynn6qmryn8wqda7b83sr51dpgblay83jcbaq")))) + "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) -- cgit v1.2.3 From dfb78fd76e4b6086506d96166b786b50923527fc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-aspli: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-aspli): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03d364da0f..29d44e05c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2525,13 +2525,13 @@ (define-public r-asgsca (define-public r-aspli (package (name "r-aspli") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz")))) + "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 930fab74f2a3ec3beec9574f2803babc62ac1c56 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-assessorf: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-assessorf): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29d44e05c1..d32af21ea3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2573,13 +2573,13 @@ (define-public r-aspli (define-public r-assessorf (package (name "r-assessorf") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7")))) + "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a1dbd6b2da3d77190974bcad1636df022e32a28b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-asset: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-asset): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d32af21ea3..736ac2c2bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2602,13 +2602,13 @@ (define-public r-assessorf (define-public r-asset (package (name "r-asset") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg")))) + "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) -- cgit v1.2.3 From 110ac40dea8267060de1394c3d812316326d708c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-atena: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-atena): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 736ac2c2bc..f5f0a9dddf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2629,13 +2629,13 @@ (define-public r-asset (define-public r-atena (package (name "r-atena") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp")))) + "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f185d3f68069ce2641087f17fe853fcfaf1d9ad8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-atsnp: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-atsnp): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5f0a9dddf..11f13383f8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2670,13 +2670,13 @@ (define-public r-atena (define-public r-atsnp (package (name "r-atsnp") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz")))) + "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 381907d25d3d4595c163ee9dc6f4274c869e9285 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-attract: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-attract): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11f13383f8..ec22a75d44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2703,13 +2703,13 @@ (define-public r-atsnp (define-public r-attract (package (name "r-attract") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82")))) + "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From faddfa8aed1c4441e58b28230a22338383325cb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: gnu: r-awfisher: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-awfisher): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec22a75d44..c1ea60490a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2734,13 +2734,13 @@ (define-public r-attract (define-public r-awfisher (package (name "r-awfisher") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1")))) + "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7bb05be10ac5d154bb552c6f18f3f8c1139a970c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-awst: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-awst): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1ea60490a..b2a0baafc1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2758,13 +2758,13 @@ (define-public r-awfisher (define-public r-awst (package (name "r-awst") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav")))) + "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) -- cgit v1.2.3 From e9a7c42deb2f4564eb75ff85998db46c111ef6f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-baalchip: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-baalchip): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2a0baafc1..d67d57bafd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2785,13 +2785,13 @@ (define-public r-awst (define-public r-baalchip (package (name "r-baalchip") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl -- cgit v1.2.3 From 91d928706ab51d1bb43300c6ffee4c77dd713db9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-basespacer: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-basespacer): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d67d57bafd..81494b4c47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2825,13 +2825,13 @@ (define-public r-baalchip (define-public r-basespacer (package (name "r-basespacer") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj")))) + "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) -- cgit v1.2.3 From 5fd038bd49ba23e093e8177cf78ce16f5e43ddff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-bac: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bac): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81494b4c47..a46e5ee721 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2848,13 +2848,13 @@ (define-public r-basespacer (define-public r-bac (package (name "r-bac") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BAC" version)) (sha256 (base32 - "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2")))) + "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6")))) (properties `((upstream-name . "BAC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BAC") -- cgit v1.2.3 From 25104e7a6b27537ceb249eff3229b7fed7df43f3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-bader: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-bader): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a46e5ee721..f6e402a742 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2872,13 +2872,13 @@ (define-public r-bac (define-public r-bader (package (name "r-bader") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm")))) + "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") -- cgit v1.2.3 From 5b4f7d11ae809b3d741d13d8f139624dfe49d416 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-badregionfinder: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6e402a742..831b508f04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2896,13 +2896,13 @@ (define-public r-bader (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9")))) + "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f07c0d00cde6ea625a752d9cdafc4adee9cf8053 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-bambu: Update to 3.0.1. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 831b508f04..d79af55592 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2923,13 +2923,13 @@ (define-public r-badregionfinder (define-public r-bambu (package (name "r-bambu") - (version "2.2.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w")))) + "08vh0vbmjn1kzp10yrinn0p0ab2cjhgiagx1vhci5sf4s6p20vy4")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f3038efb80302ab424f3d06c0e29582a384f0880 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-bandits: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79af55592..4914a1c6ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2966,13 +2966,13 @@ (define-public r-bambu (define-public r-bandits (package (name "r-bandits") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9")))) + "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c0324417728ff5d9df5e5f4e79db1bd5a331b9f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-banocc: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-banocc): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4914a1c6ca..30db1afe62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3004,13 +3004,13 @@ (define-public r-bandits (define-public r-banocc (package (name "r-banocc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx")))) + "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6af37707879ce323871120de6ced9c3767498ba2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-barcodetrackr: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-barcodetrackr): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30db1afe62..0f56190874 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3032,13 +3032,13 @@ (define-public r-banocc (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3")))) + "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9e0e4bf347254a8de565db327e2fa3aeaa52f7f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-biocversion: Update to 3.16.0. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f56190874..669af69ec8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3074,14 +3074,14 @@ (define-public r-barcodetrackr (define-public r-biocversion (package (name "r-biocversion") - (version "3.15.2") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) + "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") -- cgit v1.2.3 From 176e20a1f1d5c5f96da64efb337d100279b4ecb3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-biocgenerics: Update to 0.44.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 669af69ec8..dd3ee3b02b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3094,13 +3094,13 @@ (define-public r-biocversion (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) + "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From 2bfc463a42d6c1fb12945a1669b9d851f7114410 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-coverageview: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd3ee3b02b..a3fb0da6af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3114,13 +3114,13 @@ (define-public r-biocgenerics (define-public r-coverageview (package (name "r-coverageview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) + "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors -- cgit v1.2.3 From f0ed6c519c45978f378c9ce887302ddc773866cb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: gnu: r-cummerbund: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3fb0da6af..358eb57622 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3141,13 +3141,13 @@ (define-public r-coverageview (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) + "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From f5118505f7213fee8d6daee1fbfc3de803dde603 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-dama: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-dama): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 358eb57622..5a0c11fa10 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3171,13 +3171,13 @@ (define-public r-cummerbund (define-public r-dama (package (name "r-dama") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m")))) + "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) -- cgit v1.2.3 From 3a9089522827cf0f3138a3e6c4ce2cf82459ce0e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-damefinder: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-damefinder): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a0c11fa10..aef30bed3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3193,13 +3193,13 @@ (define-public r-dama (define-public r-damefinder (package (name "r-damefinder") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf")))) + "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 00400127ef258c5c7eca6e07d14ff3027d883867 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-dearseq: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-dearseq): Update to 1.10.0. [propagated-inputs]: Add r-scattermore. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aef30bed3a..e23df56360 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3234,14 +3234,14 @@ (define-public r-damefinder (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.4") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl")))) + "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -3254,6 +3254,7 @@ (define-public r-dearseq r-pbapply r-reshape2 r-rlang + r-scattermore r-statmod r-survey r-tibble -- cgit v1.2.3 From e3262cc2e1c8add758c6510ee37d3fa3231c694e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-debcam: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-debcam): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e23df56360..f156b010c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3273,13 +3273,13 @@ (define-public r-dearseq (define-public r-debcam (package (name "r-debcam") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) (properties `((upstream-name . "debCAM"))) (build-system r-build-system) (inputs (list openjdk)) -- cgit v1.2.3 From bd622e1464dcee788decbc05e4c1c6a1b70a19c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-decipher: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-decipher): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f156b010c5..ec7ba3136d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3312,13 +3312,13 @@ (define-public r-debcam (define-public r-decipher (package (name "r-decipher") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) + "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1")))) (build-system r-build-system) (propagated-inputs (list r-biostrings -- cgit v1.2.3 From 483084b7f9b6568b42e166e543ac85c1c22b9258 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-deco: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-deco): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec7ba3136d..24f7023365 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3336,13 +3336,13 @@ (define-public r-decipher (define-public r-deco (package (name "r-deco") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deco" version)) (sha256 (base32 - "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m")))) + "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw")))) (properties `((upstream-name . "deco"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8fd5bbc31e11d482a56b52e78ace271c62f8b7bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-decomplexdisease: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-decomplexdisease): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24f7023365..e9aaadee4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3378,13 +3378,13 @@ (define-public r-deco (define-public r-decomplexdisease (package (name "r-decomplexdisease") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEComplexDisease" version)) (sha256 (base32 - "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d")))) + "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh")))) (properties `((upstream-name . "DEComplexDisease"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9b717bcad9278bd9b6a89ced348192590ed90382 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-decomptumor2sig: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-decomptumor2sig): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e9aaadee4e..fd2846a755 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3411,13 +3411,13 @@ (define-public r-decomplexdisease (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl -- cgit v1.2.3 From 36c940a4d7bf190a8e9423fcfbcfdcdc2f9aade5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-deconrnaseq: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-deconrnaseq): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd2846a755..081c860572 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3454,13 +3454,13 @@ (define-public r-decomptumor2sig (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6")))) + "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f7dd1e4552a6131d82e91d57ece662fa08f2834f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-decontam: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-decontam): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 081c860572..52bea2703d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3481,13 +3481,13 @@ (define-public r-deconrnaseq (define-public r-decontam (package (name "r-decontam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9")))) + "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d3f0d2abe487e3e4bb62c4e7b12f1cf5f4a545c5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-deconvr: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52bea2703d..bdd1578c94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3507,13 +3507,13 @@ (define-public r-decontam (define-public r-deconvr (package (name "r-deconvr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + "14cxrcv5q6w20bq2pbxj75c0lzz96dxwqh1hqh2cl8nvvfi70jsv")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ef81f5f55e8c408c162665afc68951991f44afa0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-decoupler: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-decoupler): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdd1578c94..538fce5bde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3551,13 +3551,13 @@ (define-public r-deconvr (define-public r-decoupler (package (name "r-decoupler") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b8f0bf3e4d4cb9cf67da214af70d6719c1a901e9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: gnu: r-deepsnv: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 538fce5bde..43ce067006 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3592,13 +3592,13 @@ (define-public r-decoupler (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn")))) + "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2e48b8b0289844d08621b14af11cff297bb08cea Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-delayedarray: Update to 0.24.0. * gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43ce067006..44d37db1da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3628,13 +3628,13 @@ (define-public r-deepsnv (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) + "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From c7bf9a1a58a4edc2c428f2395d45f537ba78a65b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-derfinderhelper: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44d37db1da..02c59dd88d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3658,13 +3658,13 @@ (define-public r-delayedarray (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) + (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From de72bdab94c7a02b200693c30a1e12a3d2639086 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-drimseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-drimseq): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02c59dd88d..b3cc3823df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3683,13 +3683,13 @@ (define-public r-derfinderhelper (define-public r-drimseq (package (name "r-drimseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) + (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 81ba7cc7324a2043523b4d6cad76d34e8dc2a7ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-bluster: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-bluster): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b3cc3823df..74db2fc534 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3718,13 +3718,13 @@ (define-public r-drimseq (define-public r-bluster (package (name "r-bluster") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) + "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2564b7bcff739d5c395fe6b03d4a15c672c61e3e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-ideoviz: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74db2fc534..3e1a22cca4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3748,13 +3748,13 @@ (define-public r-bluster (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) + "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From e73a833dd25223de684ed6bbd6454e12e2724308 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-infercnv: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-infercnv): Update to 1.14.0. [propagated-inputs]: Remove r-leiden and r-reshape. Add r-igraph, r-reshape2, and r-seurat. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e1a22cca4..04dbd0f8e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3772,14 +3772,14 @@ (define-public r-ideoviz (define-public r-infercnv (package (name "r-infercnv") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -3803,15 +3803,16 @@ (define-public r-infercnv r-gplots r-gridextra r-hiddenmarkov - r-leiden + r-igraph r-matrix r-paralleldist r-phyclust r-rann r-rcolorbrewer - r-reshape + r-reshape2 r-rjags r-singlecellexperiment + r-seurat r-summarizedexperiment r-tidyr)) (native-inputs (list r-knitr)) -- cgit v1.2.3 From cc0464f5308941c50924e22749ab51099f2e7c2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-iranges: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-iranges): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 04dbd0f8e7..c2a4b67e60 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3832,13 +3832,13 @@ (define-public r-infercnv (define-public r-iranges (package (name "r-iranges") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3")))) + "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 4daec4dc4d583882dd4105599c92671bc899a6a5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-isoformswitchanalyzer: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2a4b67e60..11052c38d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3860,13 +3860,13 @@ (define-public r-iranges (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) + (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b7359c3b172981e5e195ce920125c878ac023a6a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affy: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-affy): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11052c38d2..bb7488b58b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4062,14 +4062,14 @@ (define-public r-nmf (define-public r-affy (package (name "r-affy") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) + "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj")))) (build-system r-build-system) (propagated-inputs (list r-affyio -- cgit v1.2.3 From 7034dcc2d60a8a916f37873d3e2992b8da5682f4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affycomp: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb7488b58b..197d9287eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4090,14 +4090,14 @@ (define-public r-affy (define-public r-affycomp (package (name "r-affycomp") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) + "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) -- cgit v1.2.3 From ceb39bfb391df230336e7f81cfc4e1b57cdfa3c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affycompatible: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 197d9287eb..6f1b79e188 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4111,14 +4111,14 @@ (define-public r-affycomp (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) + "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) -- cgit v1.2.3 From 6e2871262c7923cda93dcec363af39ed9465111b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affycontam: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f1b79e188..e306671e73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4156,14 +4156,14 @@ (define-public r-affycompatible (define-public r-affycontam (package (name "r-affycontam") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) + "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9947e412aca538d1690375d7a75b99622515a1e2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affycoretools: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e306671e73..847890c6a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4179,14 +4179,14 @@ (define-public r-affycontam (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) + "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 45c83ffbe587be9a84c6f48c68a2bcff1e910111 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: gnu: r-affyio: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-affyio): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 847890c6a1..f60e3569cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4221,14 +4221,14 @@ (define-public r-affycoretools (define-public r-affyio (package (name "r-affyio") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) + "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) -- cgit v1.2.3 From 261e3c12c2546e6987251af136ef3e6207c7bbf6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-affxparser: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f60e3569cb..1561c6be05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4245,14 +4245,14 @@ (define-public r-affyio (define-public r-affxparser (package (name "r-affxparser") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) + "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") -- cgit v1.2.3 From dc8c3024c0e66e40ff66dbafc06d48811b2c4ce6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-annotate: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1561c6be05..e5e3085226 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4273,14 +4273,14 @@ (define-public r-affxparser (define-public r-annotate (package (name "r-annotate") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) + "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 89f6d1d425e4fef70d181fb5b1cba13db8da2ed3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-annotationdbi: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5e3085226..8fca3ab9e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4300,13 +4300,13 @@ (define-public r-annotate (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) + "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 748599dc6bdce786608c02266218daed46697ea1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-annotationfilter: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fca3ab9e3..b000df4b84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4330,13 +4330,13 @@ (define-public r-annotationdbi (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) + "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit v1.2.3 From 065fdc2bb1d64b33b09817e63cbee67f760759f5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-annotationforge: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b000df4b84..d3553c6f2c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4355,14 +4355,14 @@ (define-public r-annotationfilter (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v")))) + "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From c5bcfef62832e7cd0900041fd1b317f585954e85 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-annotationhub: Update to 3.6.0. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3553c6f2c..37d9473063 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4387,14 +4387,14 @@ (define-public r-annotationforge (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) + "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 203ddafa090e80c048852af8b9ca15ee9d0112bc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-aroma-light: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37d9473063..f6adcaa72a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4428,14 +4428,14 @@ (define-public r-annotationhub (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) + "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 822ad274c96e52a6da5122e2e26fc48b2f8017a7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-bamsignals: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6adcaa72a..b847ea5c0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4452,14 +4452,14 @@ (define-public r-aroma-light (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) + "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics -- cgit v1.2.3 From a0d2db2e08c32cb5ce1563d09cda8f36287567a8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-biobase: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-biobase): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b847ea5c0f..320b611639 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4482,13 +4482,13 @@ (define-public r-bamsignals (define-public r-biobase (package (name "r-biobase") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) + "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From 1ef39d3d28420979fa566bafb7bde45156252b4a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-biomart: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 320b611639..9aa18d8d76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4504,13 +4504,13 @@ (define-public r-biobase (define-public r-biomart (package (name "r-biomart") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) + "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From 9048d502dab1a18091ee652671a7c88e9eaffe0a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-biocparallel: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.1. [arguments]: Update 'make-reproducible' to released files. [propagated-inputs]: Add r-cpp11. --- gnu/packages/bioconductor.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9aa18d8d76..ad26fbe153 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4589,13 +4589,13 @@ (define-public r-biomartr (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.30.3") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92")))) + "1fkfbs0n0sdssli7ibrswkfag080kgv8n1zf6ssxx729g1fz3m3h")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -4607,18 +4607,16 @@ (define-public r-biocparallel ;; Remove generated documentation. (for-each delete-file '("inst/doc/BiocParallel_BatchtoolsParam.pdf" - "inst/doc/Introduction_To_BiocParallel.pdf" "inst/doc/Errors_Logs_And_Debugging.pdf" "inst/doc/BiocParallel_BatchtoolsParam.R" "inst/doc/Introduction_To_BiocParallel.R" - "inst/doc/Errors_Logs_And_Debugging.R")) + "inst/doc/Errors_Logs_And_Debugging.R" + "inst/doc/Random_Numbers.R")) ;; Remove time-dependent macro (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" - "inst/doc/Introduction_To_BiocParallel.Rnw" "inst/doc/Errors_Logs_And_Debugging.Rnw" "vignettes/BiocParallel_BatchtoolsParam.Rnw" - "vignettes/Introduction_To_BiocParallel.Rnw" "vignettes/Errors_Logs_And_Debugging.Rnw") (("\\today") "later")) @@ -4628,7 +4626,7 @@ (define-public r-biocparallel (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-bh r-codetools r-futile-logger r-snow)) + (list r-bh r-cpp11 r-codetools r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") -- cgit v1.2.3 From 30f2fc13c659424681763a9bb3b49cc8c123f641 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: gnu: r-biostrings: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad26fbe153..a1679fa59d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4640,13 +4640,13 @@ (define-public r-biocparallel (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.1") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33")))) + "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From 3e945a87e0446da41a99cf9db6986bcfc6e699fa Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-biovizbase: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1679fa59d..519134a52c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4668,14 +4668,14 @@ (define-public r-biostrings (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) + "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bebf55cbd6c7a12390fd8bcfc2def36311a2522b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-bsgenome: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.66.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 519134a52c..2c706775f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4710,13 +4710,13 @@ (define-public r-biovizbase (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.64.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) + "1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From 9d8107b4d79fb876a15c5923b30a9e14d9a424dc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-category: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-category): Update to 2.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c706775f2..e38685b6a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4741,14 +4741,14 @@ (define-public r-bsgenome (define-public r-category (package (name "r-category") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) + "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 32629c01ef4f91e2ad3d774960626f396ea94e30 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-chipseeker: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e38685b6a4..74427343ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4772,13 +4772,13 @@ (define-public r-category (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf")))) + "1s90q73lldnmh2nxyb36hv44s3pj2l7pr0qka0z27b3cmnhqh50z")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From bfed8f183db3b643ce1d625cff28a3860bc2aa8d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-chipseq: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-chipseq): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74427343ef..41abb0b9de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4819,14 +4819,14 @@ (define-public r-chipseeker (define-public r-chipseq (package (name "r-chipseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) + "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics -- cgit v1.2.3 From ba197ae9883a213a832591a739e02cf5f404f7b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-complexheatmap: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41abb0b9de..4465776733 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4845,14 +4845,14 @@ (define-public r-chipseq (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8")))) + "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) -- cgit v1.2.3 From 539a39c4ef171d9dca2ef1a15ee164ee236b0870 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-copywriter: Update to 2.29.0. * gnu/packages/bioconductor.scm (r-copywriter): Update to 2.29.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4465776733..4b269d5877 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4885,14 +4885,14 @@ (define-public r-complexheatmap (define-public r-copywriter (package (name "r-copywriter") - (version "2.28.0") + (version "2.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) + "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ecd3d1ca6310a3e468fa845c747ec2ed2b817b08 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-deseq2: Update to 1.38.1. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b269d5877..07d4c742fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4956,14 +4956,14 @@ (define-public r-deseq (define-public r-deseq2 (package (name "r-deseq2") - (version "1.36.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) + "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 16973c9796225aeeb6f055c36b00fd1381269b13 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-dexseq: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-dexseq): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07d4c742fe..8704f9be56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4994,14 +4994,14 @@ (define-public r-deseq2 (define-public r-dexseq (package (name "r-dexseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) + "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1e5a6a9fb2a8912435fd79b07847a06c55c8ab4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-diffcyt: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-diffcyt): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8704f9be56..4e4f040a36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5039,13 +5039,13 @@ (define-public r-dexseq (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) + (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0d9a766fa783a32b74b20d6fc3d867ecddd5229a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-dirichletmultinomial: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e4f040a36..68ee7a6624 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5077,14 +5077,14 @@ (define-public r-diffcyt (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) + "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit v1.2.3 From 3a15509cb62170161d2641180de4c32c557f9172 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-dittoseq: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-dittoseq): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68ee7a6624..ee42697acc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5104,13 +5104,13 @@ (define-public r-dirichletmultinomial (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4")))) + "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bd76f479de43c71ddc53993466d68280ecbafe44 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-edaseq: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-edaseq): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee42697acc..5dc846a018 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5148,14 +5148,14 @@ (define-public r-dittoseq (define-public r-edaseq (package (name "r-edaseq") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) + "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4eb513e7dff1a422622b7083d926282be7f684c1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: gnu: r-edger: Update to 3.40.0. * gnu/packages/bioconductor.scm (r-edger): Update to 3.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5dc846a018..2e54aaf557 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5188,13 +5188,13 @@ (define-public r-edaseq (define-public r-edger (package (name "r-edger") - (version "3.38.4") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6")))) + "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From aad9a5337c46dc28b9db51b221f4155a9df6c965 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-ensembldb: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e54aaf557..ed5c38fe80 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5213,14 +5213,14 @@ (define-public r-edger (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc")))) + "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 3ff9f819f7268c1ebe61f8397f2bf035fc2605b6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-fastseg: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-fastseg): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed5c38fe80..77479105c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5258,14 +5258,14 @@ (define-public r-ensembldb (define-public r-fastseg (package (name "r-fastseg") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) + "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges -- cgit v1.2.3 From 0c1edd86f2abe07c382989aadaca955a8a1b5b1e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-gage: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-gage): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77479105c4..e815e74d4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5285,14 +5285,14 @@ (define-public r-fastseg (define-public r-gage (package (name "r-gage") - (version "2.46.1") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl")))) + "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) -- cgit v1.2.3 From b6117c18376174cb0909d5395d176f4473481437 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genefilter: Update to 1.80.0. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e815e74d4a..178f6dda23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5313,14 +5313,14 @@ (define-public r-gage (define-public r-genefilter (package (name "r-genefilter") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) + "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) -- cgit v1.2.3 From 533a3d991437b452a10190a941b3226f70e685b5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-geneoverlap: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 178f6dda23..fbba61675b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5337,13 +5337,13 @@ (define-public r-genefilter (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) + "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) -- cgit v1.2.3 From 4e501fbb67f0119f93a77cc0abefc786424a4c88 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomation: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomation): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbba61675b..aca0622f1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5356,13 +5356,13 @@ (define-public r-geneoverlap (define-public r-genomation (package (name "r-genomation") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) + "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings -- cgit v1.2.3 From c7c3bfa2500f94f198036f75080ad23f291ce70e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomeinfodb: Update to 1.34.3. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aca0622f1e..116893e53e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5403,13 +5403,13 @@ (define-public r-genomation (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.4") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v")))) + "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From d7e456cc1314eec5236b72b249e7af57a394525a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomicalignments: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 116893e53e..8ebc1453c7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5430,13 +5430,13 @@ (define-public r-genomeinfodb (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz")))) + "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From f2910e5604c153019074d529e6c08c00e67ab731 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomicfeatures: Update to 1.50.2. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ebc1453c7..63d96e73d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5463,13 +5463,13 @@ (define-public r-genomicalignments (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.4") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v")))) + "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 437ad93ce70593865c0a02d2748f2971ad0b8a16 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomicfiles: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63d96e73d9..07bd111c67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5507,14 +5507,14 @@ (define-public r-genomicfeatures (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) + "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 169c0b7fa18c049e840b4ab09b4751de08146d09 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-genomicranges: Update to 1.50.1. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.50.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07bd111c67..e7472601ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5541,13 +5541,13 @@ (define-public r-genomicfiles (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.48.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) + "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 25c5901adcccaf80a6cc8965f7fc43cb46f65a87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-gostats: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-gostats): Update to 2.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7472601ac..8db8db22b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5568,14 +5568,14 @@ (define-public r-genomicranges (define-public r-gostats (package (name "r-gostats") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) + "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 60724024de37ca8cb17c5570893ab6c755521877 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-gseabase: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-gseabase): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8db8db22b9..06e8b2ab8b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5599,14 +5599,14 @@ (define-public r-gostats (define-public r-gseabase (package (name "r-gseabase") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) + "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From aa0e18c1be20be15ab87b9a10f74169981a1dc5a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: gnu: r-hpar: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 06e8b2ab8b..51c62d8082 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5628,14 +5628,14 @@ (define-public r-gseabase (define-public r-hpar (package (name "r-hpar") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) + "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From ce2688cd3b55fb7b139731a70c4cf1b4caf5e34b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-rhtslib: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-rhtslib): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51c62d8082..eda692f087 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5648,14 +5648,14 @@ (define-public r-hpar (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.28.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) + "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, -- cgit v1.2.3 From aa25663162f29d5a4323f7c4fd5643906e76c463 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-impute: Update to 1.72.1. * gnu/packages/bioconductor.scm (r-impute): Update to 1.72.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eda692f087..f8ec6b674b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5677,13 +5677,13 @@ (define-public r-rhtslib (define-public r-impute (package (name "r-impute") - (version "1.70.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) + "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) (native-inputs (list gfortran)) (build-system r-build-system) -- cgit v1.2.3 From 1ba8e9e75c1c261c51836b69b424c5ed025db38a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-interactivedisplaybase: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8ec6b674b..d3562f45ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5697,14 +5697,14 @@ (define-public r-impute (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) + "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit v1.2.3 From 6bf50ca57a6d6a98946460a25c7601a4fc753bd4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-keggrest: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3562f45ce..732fefd78e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5722,14 +5722,14 @@ (define-public r-interactivedisplaybase (define-public r-keggrest (package (name "r-keggrest") - (version "1.36.3") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni")))) + "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 413f96c95f122ac2ab79440a230f64c38977e16b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-lfa: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 732fefd78e..a1664b4c51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5746,13 +5746,13 @@ (define-public r-keggrest (define-public r-lfa (package (name "r-lfa") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) + (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) -- cgit v1.2.3 From 0a699ea1820810ea268fcb9e8c22957db52227b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-limma: Update to 3.54.0. * gnu/packages/bioconductor.scm (r-limma): Update to 3.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1664b4c51..ee67171697 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5767,13 +5767,13 @@ (define-public r-lfa (define-public r-limma (package (name "r-limma") - (version "3.52.4") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h")))) + "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 4fd64b03b4276a625e329f1d83002768c2cfa710 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-made4: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-made4): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee67171697..ec35709503 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5786,13 +5786,13 @@ (define-public r-limma (define-public r-made4 (package (name "r-made4") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5")))) + "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fa0eda6e3f92113eb9f6f4772a3e960d6cb0d5ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-methylkit: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-methylkit): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec35709503..ae33cd6120 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5815,13 +5815,13 @@ (define-public r-made4 (define-public r-methylkit (package (name "r-methylkit") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) + "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cb7e5ebd548819921eb8f169564633d9273b8b77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-muscat: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-muscat): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae33cd6120..be80567407 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5889,14 +5889,14 @@ (define-public r-motifrg (define-public r-muscat (package (name "r-muscat") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd")))) + "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a7936348db6c609636c5366b6276898f5d149173 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-mutationalpatterns: Update to 3.8.0. * gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be80567407..2c93f79ffe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5939,14 +5939,14 @@ (define-public r-muscat (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) + "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From 66edbf1635f02c6891454061107d510e8076d9b7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-msnbase: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c93f79ffe..3bc4d2048b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5985,14 +5985,14 @@ (define-public r-mutationalpatterns (define-public r-msnbase (package (name "r-msnbase") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) + "16apm4qn7sbv06pk2i8k5z7qgkv0yq0h8ri32vikdplqxxh7h0cz")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 57ae5f71966da19ad7fb2c562070f59fc1c56f40 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-msnid: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-msnid): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bc4d2048b..f36378178e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6030,14 +6030,14 @@ (define-public r-msnbase (define-public r-msnid (package (name "r-msnid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) + "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 8735f1099568fab671e11f435eed09b7919ad096 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: gnu: r-mzid: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-mzid): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f36378178e..c645d94913 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6087,14 +6087,14 @@ (define-public r-msnid (define-public r-mzid (package (name "r-mzid") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) + "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0fbb12153b46c2c966dacef07cb77dae2b917cef Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-mzr: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-mzr): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c645d94913..c53ed569fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6118,14 +6118,14 @@ (define-public r-mzid (define-public r-mzr (package (name "r-mzr") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) + "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) -- cgit v1.2.3 From 66f1939df5b654066b52a9fa827839d186c42b31 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-organism-dplyr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-organism-dplyr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c53ed569fc..cd1fd1cec9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6169,14 +6169,14 @@ (define-public r-mzr (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7c8829ae33b8ac70bc31264e1e22c4d0a0b7ff3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-organismdbi: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd1fd1cec9..0a3475af54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6208,14 +6208,14 @@ (define-public r-organism-dplyr (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) + "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 34b615e3e755861762f9d6ad97daed47227549df Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-pcaexplorer: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a3475af54..1f9613164f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6240,14 +6240,14 @@ (define-public r-organismdbi (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) + "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cf106821f527ead0a3f26d91eaf367051e87a9a4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-pcamethods: Update to 1.90.0. * gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.90.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f9613164f..ee62d6da28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6295,14 +6295,14 @@ (define-public r-pcaexplorer (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.88.0") + (version "1.90.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) + "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dd27fffd32d252699809680842a574698058f917 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-protgenerics: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee62d6da28..6a2b97f226 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6364,14 +6364,14 @@ (define-public r-pscbs (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) + "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit v1.2.3 From 4e861e7f9a1a29fa68fda2ef803143c9dcfd9a34 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rbgl: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-rbgl): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a2b97f226..7f3dea4d3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6384,14 +6384,14 @@ (define-public r-protgenerics (define-public r-rbgl (package (name "r-rbgl") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) + "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b7ec827477ed4a7d050fa73eda583981843fce60 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rcas: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rcas): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7f3dea4d3d..7582823bcf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6406,13 +6406,13 @@ (define-public r-rbgl (define-public r-rcas (package (name "r-rcas") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) + "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 607eae1e56e74a76958dee160a04005e3264ff87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-regioner: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7582823bcf..2ec3b7096b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6456,14 +6456,14 @@ (define-public r-rcas (define-public r-regioner (package (name "r-regioner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) + "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c45dc1e27347143334d36068602df1da962dd708 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-reportingtools: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ec3b7096b..1a33a3a438 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6487,14 +6487,14 @@ (define-public r-regioner (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) + "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) -- cgit v1.2.3 From dfec056be2b6e4c7caeff097fe5eb2cfb80ebade Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rhdf5: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a33a3a438..ba65a12d41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6537,13 +6537,13 @@ (define-public r-reportingtools (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) + "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) -- cgit v1.2.3 From a7afc50aa3eff5fc316cd2e2cce88d7433a2ffec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rhdf5filters: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba65a12d41..e48aca38fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6564,14 +6564,14 @@ (define-public r-rhdf5 (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) + "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 39c52a42bda3e72324282fce1acd7b6a5936c29b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rsamtools: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e48aca38fa..b7301b548d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6590,13 +6590,13 @@ (define-public r-rhdf5filters (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) + "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From 855ea2a8f1b37131e0590adbce114131b1ac4d9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: gnu: r-rtracklayer: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7301b548d..e920111b24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6655,13 +6655,13 @@ (define-public r-restfulr (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) + "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From d6fac1138fb7f09f4d34739d96cb4156db8e487a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-scannotatr: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e920111b24..4529213c04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6734,13 +6734,13 @@ (define-public r-samr (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) + (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4d8a2f5562eb8901543380d8773f9fccacdcc414 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-scdblfinder: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4529213c04..c95b0fa304 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6771,13 +6771,13 @@ (define-public r-scannotatr (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) + (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6fb3733394d1bbd684b20b79c4d8fd633481c84f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-scmap: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c95b0fa304..3e0e5da87b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6816,13 +6816,13 @@ (define-public r-scdblfinder (define-public r-scmap (package (name "r-scmap") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 06856951557e0b31e7c2653459ba98fabe72168c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-scry: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-scry): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e0e5da87b..e4470ea30e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6858,13 +6858,13 @@ (define-public r-scmap (define-public r-scry (package (name "r-scry") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193")))) + "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 59e810b232eb248f567eb582f5549320abfc3eb3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-seqlogo: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4470ea30e..5a220a8558 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6890,14 +6890,14 @@ (define-public r-scry (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) + "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 1ca80ed5a5aa494e70ac02f7a38da5d2cfe24ece Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-seqpattern: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a220a8558..e289ead24f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6913,13 +6913,13 @@ (define-public r-seqlogo (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) + "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit v1.2.3 From 94af5e4e968456440599051efb8dd413e261f04b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-shortread: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e289ead24f..70be2c7a77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6936,14 +6936,14 @@ (define-public r-seqpattern (define-public r-shortread (package (name "r-shortread") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) + "0z700mjll3zv3451rd6p5195w0g3rmw17xddc5qwflwm8dnhdmll")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From e5e22f33526ef2c1c27e1845d47e8e0622b9dd9c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-simplifyenrichment: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70be2c7a77..a99a5e2490 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6979,14 +6979,14 @@ (define-public r-shortread (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) + "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) -- cgit v1.2.3 From 2c821d2ce56ba65b30f240b7b64c5666d8d5023c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-transcriptr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a99a5e2490..fd357c2d0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7020,13 +7020,13 @@ (define-public r-simplifyenrichment (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) + (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c07b603d6474ae89b0bc04c2bbb281600975c379 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-trajectoryutils: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd357c2d0b..b345a33a6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7070,14 +7070,14 @@ (define-public r-transcriptr (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) + "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) -- cgit v1.2.3 From e4e4b97a67ff08c03f148f2afb7f09ac6d439ac6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-slingshot: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-slingshot): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b345a33a6f..71eb6128ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7097,13 +7097,13 @@ (define-public r-trajectoryutils (define-public r-slingshot (package (name "r-slingshot") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) + "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33")))) (build-system r-build-system) (propagated-inputs (list r-igraph -- cgit v1.2.3 From 3f307e6ebc6eb4bad878aa5fc744d401b105f4a7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-stager: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-stager): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71eb6128ac..1a5f81d3bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7129,13 +7129,13 @@ (define-public r-slingshot (define-public r-stager (package (name "r-stager") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) + (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) -- cgit v1.2.3 From 3b89c301db466712dd9c5d4b00b2bd291048d93c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: gnu: r-stringdb: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-stringdb): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a5f81d3bf..41066c6050 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7152,13 +7152,13 @@ (define-public r-stager (define-public r-stringdb (package (name "r-stringdb") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) + (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f87a87eee849d246dd8adcc86a86a28585c67691 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-structuralvariantannotation: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41066c6050..8e1ee34adb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7185,13 +7185,13 @@ (define-public r-stringdb (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) + (base32 "11z3acsbaifrxkghd7i8503ki9s1lc6c22880yna6qcfprlzb44g")))) (build-system r-build-system) (propagated-inputs (list r-assertthat -- cgit v1.2.3 From ab4f54d5f9e8377398179f3a1e1f0feb2ce1cd3f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-summarizedexperiment: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e1ee34adb..498cf7bf03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7222,13 +7222,13 @@ (define-public r-structuralvariantannotation (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) + "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From adedfb51fa84c084a4633d6a766c005942eedb3f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-sva: Update to 3.46.0. * gnu/packages/bioconductor.scm (r-sva): Update to 3.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 498cf7bf03..38c914c71b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7256,14 +7256,14 @@ (define-public r-summarizedexperiment (define-public r-sva (package (name "r-sva") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) + "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g")))) (build-system r-build-system) (propagated-inputs (list r-edger -- cgit v1.2.3 From 8ded00c7dacf7f7b92ecb03def20e190e1da5c4b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-systempiper: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-systempiper): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38c914c71b..87b6c90d40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7287,14 +7287,14 @@ (define-public r-sva (define-public r-systempiper (package (name "r-systempiper") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) + "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 88440606c76f027e3aa3d3214648f4af305e45c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-topgo: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-topgo): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87b6c90d40..714b3dae4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7330,13 +7330,13 @@ (define-public r-systempiper (define-public r-topgo (package (name "r-topgo") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) + "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit v1.2.3 From c1790d17fc5ca62f25c3d93c002aa4c27b2639fa Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-tximport: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 714b3dae4e..7eb5ec5541 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7363,13 +7363,13 @@ (define-public r-topgo (define-public r-tximport (package (name "r-tximport") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) + "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From 9501ec8c4c7521ae42e375c2bcd6d1bf7d1c7b64 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-variantannotation: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7eb5ec5541..4d5d9f5428 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7421,13 +7421,13 @@ (define-public r-valr (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) + "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs -- cgit v1.2.3 From 32afcf9b90b2b34720db14dc3fa232d1cd193072 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-vsn: Update to 3.66.0. * gnu/packages/bioconductor.scm (r-vsn): Update to 3.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4d5d9f5428..29ea4b313b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7459,14 +7459,14 @@ (define-public r-variantannotation (define-public r-vsn (package (name "r-vsn") - (version "3.64.0") + (version "3.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) + "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) -- cgit v1.2.3 From e03bff40fcebc2e27c1aa1e923d126b8a3f7ba2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-xina: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-xina): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29ea4b313b..b29bc13957 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7528,13 +7528,13 @@ (define-public r-xcir (define-public r-xina (package (name "r-xina") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) + (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8fe91b692a8ec5845a751560bd5597c1e848bd2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-xmapbridge: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-xmapbridge): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b29bc13957..8ba60a2821 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7564,13 +7564,13 @@ (define-public r-xina (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) + (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") -- cgit v1.2.3 From 9a707db7eeec0e68862bc3b7e0480ae3dc80fb93 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-xvector: Update to 0.38.0. * gnu/packages/bioconductor.scm (r-xvector): Update to 0.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ba60a2821..a3c3b0594a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7591,13 +7591,13 @@ (define-public r-xmapbridge (define-public r-xvector (package (name "r-xvector") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) + "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.2.3 From 7a0c779a91244af71de1ef0825582a1cfcb31ce3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-zlibbioc: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3c3b0594a..976ca0d1c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7625,13 +7625,13 @@ (define-public r-xvector (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) + "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.2.3 From 44ec429d483f6fba07c93b023ae5357f507d085a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-zellkonverter: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 976ca0d1c8..b1ded1bfb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7644,13 +7644,13 @@ (define-public r-zlibbioc (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.5") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6")))) + (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7db100f21fba0020be304b5c33b9f92db098b93f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: gnu: r-geneplotter: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1ded1bfb5..6e1a7e7b08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7676,14 +7676,14 @@ (define-public r-zellkonverter (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) + "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava")))) (build-system r-build-system) (propagated-inputs (list r-annotate -- cgit v1.2.3 From 4fba8d9d7cb92e5a5ae9bcc2ee45ed02d7270451 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-oligoclasses: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6e1a7e7b08..f03ed0a87b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7701,14 +7701,14 @@ (define-public r-geneplotter (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) + "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c05ab729668d302667c003a9f6f34ee5bb890470 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-oligo: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f03ed0a87b..ab9d08069e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7736,14 +7736,14 @@ (define-public r-oligoclasses (define-public r-oligo (package (name "r-oligo") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) + "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 11c4bc08db3afe687fa0a200642e23909fe9b1ff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-qvalue: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab9d08069e..53d2be265f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7772,14 +7772,14 @@ (define-public r-oligo (define-public r-qvalue (package (name "r-qvalue") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) + "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) -- cgit v1.2.3 From 9bb55dfa8d106648028db91f4ba807d17c46683d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-apeglm: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-apeglm): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53d2be265f..247db3c8e1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7827,13 +7827,13 @@ (define r-rcppnumerical (define-public r-apeglm (package (name "r-apeglm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) + "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6f68e3f42d13dab8cfccf4d6dd6ab6bacdc93f9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-greylistchip: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 247db3c8e1..71221d0995 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7854,13 +7854,13 @@ (define-public r-apeglm (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) + "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c5b66701679af103c2b1309f36b2e0e1ae6536b7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-diffbind: Update to 3.8.1. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71221d0995..51d7bde15c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7881,14 +7881,14 @@ (define-public r-greylistchip (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.4") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr")))) + "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d4d9ce28010197e54d0264814fd481463531d505 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-mbkmeans: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51d7bde15c..0853ae35d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7959,13 +7959,13 @@ (define-public r-ripseeker (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) + "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From 77d10366d469100306ee8330e57facb5e878b954 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-multtest: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0853ae35d3..f05ecdb04a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7991,14 +7991,14 @@ (define-public r-mbkmeans (define-public r-multtest (package (name "r-multtest") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) + "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) -- cgit v1.2.3 From 7a11e32dae9753f097d179ac6e13f741e2cd97ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-graph: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f05ecdb04a..fb95f42251 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8026,13 +8026,13 @@ (define-public r-multtest (define-public r-graph (package (name "r-graph") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) + "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) -- cgit v1.2.3 From 73add01b2293b18d2c74905d4ddc58e890831b77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-chippeakanno: Update to 3.32.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb95f42251..baa6d9fc14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8119,14 +8119,14 @@ (define-public r-codedepends (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.30.1") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y")))) + "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 03862582db4b8bd81c18fd010345fc0e15248f93 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-matrixgenerics: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index baa6d9fc14..e43cb7277b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8173,13 +8173,13 @@ (define-public r-chippeakanno (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f")))) + "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From 78d4b00882bfe42a19617e84bfa0aa3126c6b003 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-marray: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e43cb7277b..6cfb5e5549 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8200,12 +8200,12 @@ (define-public r-matrixgenerics (define-public r-marray (package (name "r-marray") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) + (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs")))) (build-system r-build-system) (propagated-inputs (list r-limma)) -- cgit v1.2.3 From 67799955b442926c87a7eb6c621f78746767fb9a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-cghbase: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6cfb5e5549..10524349ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8219,12 +8219,12 @@ (define-public r-marray (define-public r-cghbase (package (name "r-cghbase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) + (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 564afa20fb1f2093279af7cdde23335bee1ee0b6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: gnu: r-cghcall: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10524349ac..ba3f3a6dd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8238,12 +8238,12 @@ (define-public r-cghbase (define-public r-cghcall (package (name "r-cghcall") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) + (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7803ed86fe27e7e0d66ceb468dc6d5436c3e8f03 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-qdnaseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba3f3a6dd6..6249b010c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8257,12 +8257,12 @@ (define-public r-cghcall (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) + (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 721c125de4352ae56afc08e9aa43f188078eb376 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-bayseq: Update to 2.31.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.31.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6249b010c0..462bc1a23b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8289,14 +8289,14 @@ (define-public r-qdnaseq (define-public r-bayseq (package (name "r-bayseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) + "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5d32e4a62a941a94f3c1771f4669f9c0f145d55c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-chipcomp: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 462bc1a23b..796e3ffc7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8313,14 +8313,14 @@ (define-public r-bayseq (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) + "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a0465bd1162ba8a46acef4d0feadb201c48ea656 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-riboprofiling: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 796e3ffc7e..95d78ea246 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,14 +8347,14 @@ (define-public r-chipcomp (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) + "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e4ab1ac23e26f9aadd1de57b1edb5b5a0c4f0a9d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-riboseqr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 95d78ea246..24e0db5a79 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8388,14 +8388,14 @@ (define-public r-riboprofiling (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) + "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e7393c32f4d0a389e11e825858792014ede42769 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-interactionset: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24e0db5a79..42bc16b013 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8416,14 +8416,14 @@ (define-public r-riboseqr (define-public r-interactionset (package (name "r-interactionset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) + "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit v1.2.3 From 8d62cfc7d103b3e3514bd91c87e84f661e5ddcb2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-genomicinteractions: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42bc16b013..779d03b055 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8450,14 +8450,14 @@ (define-public r-interactionset (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) + "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit v1.2.3 From 74852cb46ddad51b1c092494fd1e862939089752 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-ctc: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 779d03b055..19b1e7a4b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8491,14 +8491,14 @@ (define-public r-genomicinteractions (define-public r-ctc (package (name "r-ctc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) + "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") -- cgit v1.2.3 From 7bf9521e85229245e1d235534607d5c9b7839643 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-goseq: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19b1e7a4b5..31d3256484 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8511,14 +8511,14 @@ (define-public r-ctc (define-public r-goseq (package (name "r-goseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) + "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 9b615c408f2b047f0bd1de8c035e47d7141f0b98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-glimma: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31d3256484..11e92771da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8537,14 +8537,14 @@ (define-public r-goseq (define-public r-glimma (package (name "r-glimma") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) + "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 870a334f6d4b900c571899121a73f9f425975812 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-rots: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11e92771da..751657051a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8570,14 +8570,14 @@ (define-public r-glimma (define-public r-rots (package (name "r-rots") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) + "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 83ff82481c9758a586f15533958e5ad063f088bf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-plgem: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 751657051a..84d128d92c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8593,14 +8593,14 @@ (define-public r-rots (define-public r-plgem (package (name "r-plgem") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) + "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) -- cgit v1.2.3 From 45616713a7ee3b568cf88eed950cedb9169e67c5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: gnu: r-inspect: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84d128d92c..43afa6db13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8617,14 +8617,14 @@ (define-public r-plgem (define-public r-inspect (package (name "r-inspect") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) + "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7146ee20d967f27c33d368cc8bd4790266ccccad Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-dnabarcodes: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43afa6db13..7a8a1ed0b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8663,14 +8663,14 @@ (define-public r-inspect (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) + "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c3b6219435b8dc137b6912a29ef645e68dd04d4a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-ruvseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a8a1ed0b2..7fe05ca620 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8690,14 +8690,14 @@ (define-public r-dnabarcodes (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) + "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ccd857d8cfaa11579dfe908859e49a5666079c18 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-biocneighbors: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7fe05ca620..be519958d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8715,14 +8715,14 @@ (define-public r-ruvseq (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) + "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b711b25c09b5a7bc0ac35dfb7264e6b88bcb13ce Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-scaledmatrix: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be519958d2..fd6007e1b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8743,14 +8743,14 @@ (define-public r-biocneighbors (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz")))) + "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0bb3b953eb347febb52d1c060929205259fde525 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-treeio: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-treeio): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd6007e1b9..827bc9593a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8769,14 +8769,14 @@ (define-public r-scaledmatrix (define-public r-treeio (package (name "r-treeio") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1")))) + "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3e7dbe7804b2ca9dd4c16893feb408c34578efcb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-ggtree: Update to 3.6.2. * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.6.2. [propagated-inputs]: Add r-cli. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 827bc9593a..0fc9f1f937 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8801,19 +8801,20 @@ (define-public r-treeio (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.4") + (version "3.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5")))) + "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs (list r-ape r-aplot + r-cli r-dplyr r-ggfun r-ggplot2 -- cgit v1.2.3 From c4df4af6baccf207299410838e3c23fecda026d2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-metapod: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-metapod): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fc9f1f937..58b32d8101 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8839,14 +8839,14 @@ (define-public r-ggtree (define-public r-metapod (package (name "r-metapod") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) + "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c733f330e1bb5beddeb6594909ef9444e2c1d730 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-biocsingular: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58b32d8101..829947266b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8868,14 +8868,14 @@ (define-public r-metapod (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) + "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1517a8fd4ffc24bd44fc495d59ef1d2503625885 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-destiny: Update to 3.12.0. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 829947266b..28d4a88816 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8903,14 +8903,14 @@ (define-public r-biocsingular (define-public r-destiny (package (name "r-destiny") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) + "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 1dfad3e535bb058633f98df138126cfd5dc4ec8d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-savr: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28d4a88816..8d4d71cae8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8947,14 +8947,14 @@ (define-public r-destiny (define-public r-savr (package (name "r-savr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) + "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c7f24274bf365af2458de89a22235a94c456254e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-chipexoqual: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d4d71cae8..6781d5be30 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8969,14 +8969,14 @@ (define-public r-savr (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) + "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3a731c1b28660a5742ad435032ebd23e86194710 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-copynumber: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6781d5be30..b9c5b01c5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9009,13 +9009,13 @@ (define-public r-chipexoqual (define-public r-copynumber (package (name "r-copynumber") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) + "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) -- cgit v1.2.3 From 9fcaa4e3d85025b16a44c79c8f3cf86f82642eef Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-dnacopy: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b9c5b01c5c..b4253f6f8f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9029,14 +9029,14 @@ (define-public r-copynumber (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) + "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) -- cgit v1.2.3 From c9dc9b10e844729b5a7087d84bae2a07287e09f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: gnu: r-ebseq: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4253f6f8f..ecd2387c66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9127,14 +9127,14 @@ (define-public r-nbpseq (define-public r-ebseq (package (name "r-ebseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) + "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f60faec932b564b93d09251945a1abf6dda84855 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-karyoploter: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecd2387c66..5870950f00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9149,13 +9149,13 @@ (define-public r-ebseq (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) + "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From e8e7990b881206f04258ca73986f0c9915b04363 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-lpsymphony: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5870950f00..20bfa1eb14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9187,14 +9187,14 @@ (define-public r-karyoploter (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) + "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) (build-system r-build-system) (arguments (list -- cgit v1.2.3 From 3a9e82f0f5c963895cd65c3af07e997db6ca309f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-ihw: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20bfa1eb14..ee3b1e2f62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9226,14 +9226,14 @@ (define-public r-lpsymphony (define-public r-ihw (package (name "r-ihw") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) + "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 29f0a198a5e3eb455e761288faa1904d391744f2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-icobra: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee3b1e2f62..d3a16b4b38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9255,14 +9255,14 @@ (define-public r-ihw (define-public r-icobra (package (name "r-icobra") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) + "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2896e9005e995f24d87a53791de75fb5d43af39f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-residualmatrix: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3a16b4b38..3f6d426072 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9292,14 +9292,14 @@ (define-public r-icobra (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd")))) + "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) -- cgit v1.2.3 From 9f49e6eee8cb7cc70f5bb63b69b25623ddfeeecd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-batchelor: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f6d426072..e5b1db7717 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9321,14 +9321,14 @@ (define-public r-residualmatrix (define-public r-batchelor (package (name "r-batchelor") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc")))) + "1cdpq8zfn718qmsqjp79siddh3kzag4a90p276v261xbjvrxavjv")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f149c694fda4747934269f5983b1d4a4cdd74419 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-mast: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5b1db7717..ac391d8b22 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9364,14 +9364,14 @@ (define-public r-batchelor (define-public r-mast (package (name "r-mast") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) + "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9ddd0a0ab48fb5eee11497eec8287a402d0f37d0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-monocle: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac391d8b22..4018aa54f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9399,14 +9399,14 @@ (define-public r-mast (define-public r-monocle (package (name "r-monocle") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn")))) + "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 70a1e54b8be42f6a27c8ec061c0bcdf2fe5f9636 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-noiseq: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4018aa54f1..73386d93ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9584,14 +9584,14 @@ (define-public r-monocle3 (define-public r-noiseq (package (name "r-noiseq") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) + "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7030f66362cac69dd8a7d209184f74b5c167e53a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-scdd: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73386d93ec..0d1ece3b7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9610,14 +9610,14 @@ (define-public r-noiseq (define-public r-scdd (package (name "r-scdd") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) + "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d00553da9b4f23ab3c6f4e02e92f87c4ac988097 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-scone: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d1ece3b7e..1b05269c03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9648,14 +9648,14 @@ (define-public r-scdd (define-public r-scone (package (name "r-scone") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) + "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light -- cgit v1.2.3 From 62c58299a2c5eeb992d778a703b6713ebab3637b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-geoquery: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b05269c03..1709ef8ca1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9692,14 +9692,14 @@ (define-public r-scone (define-public r-geoquery (package (name "r-geoquery") - (version "2.64.2") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) + "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e3d4563b4fbd3db1c502cf41712f809bde6c01eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-illuminaio: Update to 0.40.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1709ef8ca1..eee8b84a7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9727,14 +9727,14 @@ (define-public r-geoquery (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) + "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12")))) (build-system r-build-system) (propagated-inputs (list r-base64)) -- cgit v1.2.3 From 734d40892af3f76ce6e43cc68a4e4feb6abd5b22 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: gnu: r-siggenes: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eee8b84a7d..8639eebaa2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9748,14 +9748,14 @@ (define-public r-illuminaio (define-public r-siggenes (package (name "r-siggenes") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) + "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) -- cgit v1.2.3 From a4e446a3a3832d0ac76f4b994b38ac7becfbfcc5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-bumphunter: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8639eebaa2..1bb50f6019 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9772,14 +9772,14 @@ (define-public r-siggenes (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) + "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 3c1854108e1b121d14afaec6f89692bb22aecbad Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-microbiome: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-microbiome): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1bb50f6019..9ccb3911a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9806,13 +9806,13 @@ (define-public r-bumphunter (define-public r-microbiome (package (name "r-microbiome") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12")))) + "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 59fe138fccdb03a00c3e05c9a8d4537faedfcde3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-milor: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-milor): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9ccb3911a4..b800c4c4bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9843,13 +9843,13 @@ (define-public r-microbiome (define-public r-milor (package (name "r-milor") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs")))) + "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 44a5942ce71478848f2b238eb681e5b76d96075d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-minfi: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b800c4c4bc..7a4ed12b93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9891,14 +9891,14 @@ (define-public r-milor (define-public r-minfi (package (name "r-minfi") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) + "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc")))) (build-system r-build-system) (propagated-inputs (list r-beanplot -- cgit v1.2.3 From 6b9cb6256af20124964628ec860d288fea2209c7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-methylumi: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a4ed12b93..23c3817acb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9942,14 +9942,14 @@ (define-public r-minfi (define-public r-methylumi (package (name "r-methylumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) + "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4")))) (build-system r-build-system) (propagated-inputs (list r-annotate -- cgit v1.2.3 From 8bd75d3ef7f6e4dd7cf15fa85a6aacd659b0f2f8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-lumi: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23c3817acb..12ef4d1d90 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9989,14 +9989,14 @@ (define-public r-methylumi (define-public r-lumi (package (name "r-lumi") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) + "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq")))) (build-system r-build-system) (propagated-inputs (list r-affy -- cgit v1.2.3 From e0b3d2dda9e97b875fff38eed81906473f7404c1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-linnorm: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12ef4d1d90..323233af58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10028,14 +10028,14 @@ (define-public r-lumi (define-public r-linnorm (package (name "r-linnorm") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) + "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4c30f1a5b51af0def6fd1f452cd28a2dfc45af83 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-ioniser: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 323233af58..710dd14da9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10089,14 +10089,14 @@ (define-public r-linnorm (define-public r-ioniser (package (name "r-ioniser") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) + "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5c2e048789151155969785c42bbaf0c87292fed1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-tradeseq: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 710dd14da9..b6541c80c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10185,13 +10185,13 @@ (define-public r-metap (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) + "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 69eb260b6fe898f2afe23411d67aabdccd7a4910 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-varianttools: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6541c80c4..ed1dfb8f28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10254,14 +10254,14 @@ (define-public r-triform (define-public r-varianttools (package (name "r-varianttools") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) + "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 83fa503de34d936b93175a579bbf874a1cb76632 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-heatplus: Update to 3.6.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 3.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed1dfb8f28..c6267ed444 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10294,14 +10294,14 @@ (define-public r-varianttools (define-public r-heatplus (package (name "r-heatplus") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) + "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9171e09d3730ee7e964f05df078bc2ac286db091 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-gosemsim: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c6267ed444..5ad780d66a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10319,14 +10319,14 @@ (define-public r-heatplus (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) + "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 368fdb08506867d6067e88c7d3457d93b3c9dd39 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: gnu: r-anota: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ad780d66a..d47453e4de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10346,14 +10346,14 @@ (define-public r-gosemsim (define-public r-anota (package (name "r-anota") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) + "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) -- cgit v1.2.3 From e392bcce646ea26b1121fde0b3d4ca6800f3a552 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-sigpathway: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d47453e4de..b1f0ba24e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10376,14 +10376,14 @@ (define-public r-anota (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) + "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") -- cgit v1.2.3 From 245ab8252246bb6695f85f09d41eaef7f05446af Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-fcscan: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-fcscan): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1f0ba24e7..4a8b0ef407 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10398,13 +10398,13 @@ (define-public r-sigpathway (define-public r-fcscan (package (name "r-fcscan") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) + (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 11b8f6caf0b52262e55fb27fe7538aa233607728 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-fgsea: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.24.0. [propagated-inputs]: Remove r-gridextra. Add r-cowplot. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a8b0ef407..9402a06b77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10431,22 +10431,22 @@ (define-public r-fcscan (define-public r-fgsea (package (name "r-fgsea") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) + "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel + r-cowplot r-data-table r-fastmatch r-ggplot2 - r-gridextra r-matrix r-rcpp)) (native-inputs -- cgit v1.2.3 From 56fe11925730ec476eb93b927b56f869a9465cc9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-dose: Update to 3.24.1. * gnu/packages/bioconductor.scm (r-dose): Update to 3.24.1. [propagated-inputs]: Remove r-do-db. Add r-hdo-db. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9402a06b77..bdc729bcf9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10463,23 +10463,23 @@ (define-public r-fgsea (define-public r-dose (package (name "r-dose") - (version "3.22.1") + (version "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i")))) + "1ai42pnd8s8ws6y9nlq5d858w2rp8gfw2vpndslspj4q8gc4dbb1")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel - r-do-db r-fgsea r-ggplot2 r-gosemsim + r-hdo-db r-qvalue r-reshape2)) (native-inputs -- cgit v1.2.3 From 7d70375aa7ef257360900f8aa6a4621f80f512a2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-enrichplot: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.1. [propagated-inputs]: Add r-ggnewscale and r-rlang. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdc729bcf9..31f89ec33e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10498,20 +10498,21 @@ (define-public r-dose (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.2") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss")))) + "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggplot2 r-ggraph + r-ggnewscale r-ggtree r-gosemsim r-igraph @@ -10520,6 +10521,7 @@ (define-public r-enrichplot r-purrr r-rcolorbrewer r-reshape2 + r-rlang r-scatterpie r-shadowtext r-yulab-utils)) -- cgit v1.2.3 From 26a4a1e36b548aa7406ba8656948c2b4e0620fb0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-clusterprofiler: Update to 4.6.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.6.0. [propagated-inputs]: Add r-gson. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31f89ec33e..3d2519866e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10538,14 +10538,14 @@ (define-public r-enrichplot (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.4") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5")))) + "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -10557,6 +10557,7 @@ (define-public r-clusterprofiler r-enrichplot r-go-db r-gosemsim + r-gson r-magrittr r-plyr r-qvalue -- cgit v1.2.3 From c5c2cbe1e369d036cf3345d43c21480fe284dd5b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-clusterexperiment: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d2519866e..798c5d1db9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10576,13 +10576,13 @@ (define-public r-clusterprofiler (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) + "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From ed0238c59e81cc532fb06ce33fd9bd5d70f73850 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-mlinterfaces: Update to 1.78.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.78.0. [propagated-inputs]: Add r-summarizedexperiment. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 798c5d1db9..f873b787e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10622,14 +10622,14 @@ (define-public r-clusterexperiment (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) + "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -10652,6 +10652,7 @@ (define-public r-mlinterfaces r-rpart r-sfsmisc r-shiny + r-summarizedexperiment r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") -- cgit v1.2.3 From e8dc5aec69e03b52723849fd0d112a1a29fa14b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-annaffy: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f873b787e4..bff059f37f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10665,14 +10665,14 @@ (define-public r-mlinterfaces (define-public r-annaffy (package (name "r-annaffy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) + "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From e65450cc4c444d41c846652a753ec52c635bef0e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-a4core: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bff059f37f..e03ad9b719 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10697,14 +10697,14 @@ (define-public r-annaffy (define-public r-a4core (package (name "r-a4core") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) + "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 94a665b3470d270936da9935effd5c20f9fa9cfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-a4classif: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e03ad9b719..fcd257d672 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10721,14 +10721,14 @@ (define-public r-a4core (define-public r-a4classif (package (name "r-a4classif") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) + "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0b89230af37847a9f9522b42ffdbd185094f632d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: gnu: r-a4preproc: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fcd257d672..f1fe9f5c7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10751,14 +10751,14 @@ (define-public r-a4classif (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) + "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9e1a4ae173617463e72d7ba748f79a66787bda98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-a4reporting: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1fe9f5c7e..11a2fea2fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10775,14 +10775,14 @@ (define-public r-a4preproc (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) + "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a618ee00cdcfac07331433338f4dd703304ccf87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-a4base: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11a2fea2fa..2c8d58abeb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10799,14 +10799,14 @@ (define-public r-a4reporting (define-public r-a4base (package (name "r-a4base") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) + "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8a11bd2c1eb03329484d5fa14a7f9a6d1e956cbf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-a4: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c8d58abeb..03251c938f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10830,14 +10830,14 @@ (define-public r-a4base (define-public r-a4 (package (name "r-a4") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) + "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) -- cgit v1.2.3 From e09f43a15db7232b5a12030d8168fe11c14d4b4e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-abseqr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03251c938f..ee3d1e3397 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10851,14 +10851,14 @@ (define-public r-a4 (define-public r-abseqr (package (name "r-abseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) + "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 621c91564da6001d839454061a41b785b6810e8c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-bacon: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee3d1e3397..d6c8162ba0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10899,14 +10899,14 @@ (define-public r-abseqr (define-public r-bacon (package (name "r-bacon") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) + "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) -- cgit v1.2.3 From bdd122be5745686509220e86df3e124ecce8f699 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-rgadem: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d6c8162ba0..24da7bcd91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10924,14 +10924,14 @@ (define-public r-bacon (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.1") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q")))) + "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5fd930a771160ae3acb3f057eec3307004feb5d3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-motifdb: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24da7bcd91..9b18594439 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10978,12 +10978,12 @@ (define-public r-motiv (define-public r-motifdb (package (name "r-motifdb") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) + (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1d8e36abd902e09d934174480fff76eb2712eef8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-motifbreakr: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9b18594439..fe343c3c67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11005,12 +11005,12 @@ (define-public r-motifdb (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) + (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1acf7fdae3e67637ec54444e610b8c2b0bc15240 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-motifstack: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe343c3c67..7470d2577d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11055,14 +11055,14 @@ (define-public r-motifbreakr (define-public r-motifstack (package (name "r-motifstack") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) + "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 380c5b1894b37bebf07218faae4a02d27e09f953 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-genomicscores: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7470d2577d..e18e85f2de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11087,14 +11087,14 @@ (define-public r-motifstack (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.8.2") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j")))) + "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 82015ac5b1798d7e30f2141aeb2fef4437669a2e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-atacseqqc: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e18e85f2de..7e02a29608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11125,14 +11125,14 @@ (define-public r-genomicscores (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) + "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a2ec0390a774b8cf18609732b038919a7cb1c709 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-gofuncr: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e02a29608..47d6427d4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11172,14 +11172,14 @@ (define-public r-atacseqqc (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) + "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d48170687b8b5d32ba909a18392cc8c8384ed605 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: gnu: r-annotationtools: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47d6427d4a..8fde74acfa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11277,14 +11277,14 @@ (define-public r-annotationfuncs (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) + "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) -- cgit v1.2.3 From d0a0afe1daf245c36ec7938265d5724d2153b0f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-allelicimbalance: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fde74acfa..62d4645840 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11302,14 +11302,14 @@ (define-public r-annotationtools (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) + "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) -- cgit v1.2.3 From 265c03a7bd8c28da947ed9f621b868052c8960ae Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-aucell: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62d4645840..489f426de9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11345,14 +11345,14 @@ (define-public r-allelicimbalance (define-public r-aucell (package (name "r-aucell") - (version "1.18.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) + "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c410fa50e1fe8f83f176f1d6896b052f0e75bc98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-ebimage: Update to 4.40.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 489f426de9..c8aacd6ae6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11385,14 +11385,14 @@ (define-public r-aucell (define-public r-ebimage (package (name "r-ebimage") - (version "4.38.0") + (version "4.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) + "1k6gbivwlai451whq2vr3c0shzs9p4g188jn5waw7973gdzdi00q")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 66612f9583c7590a0428c17c923d037c3f2c431e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-yamss: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8aacd6ae6..d628baf558 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11424,14 +11424,14 @@ (define-public r-ebimage (define-public r-yamss (package (name "r-yamss") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) + "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics -- cgit v1.2.3 From a072ce0eccec3e1f5dc0f0d5500d952cf73b966a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-gtrellis: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d628baf558..a126791eb9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11457,14 +11457,14 @@ (define-public r-yamss (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) + "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) -- cgit v1.2.3 From f1a1fed1df7d1c9bd8de5c6e7cfacc811dda1f5c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-somaticsignatures: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a126791eb9..409c47c41b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11483,14 +11483,14 @@ (define-public r-gtrellis (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) + "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) -- cgit v1.2.3 From 42b297b2951838fcb1374d9cbfea65bf1c8f2da9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-yapsa: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 409c47c41b..420e0d1830 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11522,14 +11522,14 @@ (define-public r-somaticsignatures (define-public r-yapsa (package (name "r-yapsa") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) + "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4da41a5977d646927c2f4d5128b691fa554d7739 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-gcrma: Update to 2.70.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 420e0d1830..7dbc7abeb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11571,14 +11571,14 @@ (define-public r-yapsa (define-public r-gcrma (package (name "r-gcrma") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) + "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1")))) (build-system r-build-system) (propagated-inputs (list r-affy -- cgit v1.2.3 From 0ac185ebb40c06ce18d525b6a106aca8df8f3ac0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-quantro: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7dbc7abeb3..20f82d5e23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11653,14 +11653,14 @@ (define-public r-yaqcaffy (define-public r-quantro (package (name "r-quantro") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) + "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 802db22edff6eca8f55944a2d737b8d3ec22201c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-yarn: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20f82d5e23..da05c34cc0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11686,14 +11686,14 @@ (define-public r-quantro (define-public r-yarn (package (name "r-yarn") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) + "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 275fda864af90b5a6b64a8ee8de1ac61180390e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-roar: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da05c34cc0..fe80294022 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11723,14 +11723,14 @@ (define-public r-yarn (define-public r-roar (package (name "r-roar") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) + "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics -- cgit v1.2.3 From 61edc0f206718fa60d57a05f36342be6e6130376 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-massspecwavelet: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe80294022..d084b3c372 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11791,14 +11791,14 @@ (define-public r-xbseq (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) + "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) -- cgit v1.2.3 From bcc13d3642cd167767220f7ec31a85fc704ae166 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-xcms: Update to 3.20.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d084b3c372..97181dbf06 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11815,14 +11815,14 @@ (define-public r-massspecwavelet (define-public r-xcms (package (name "r-xcms") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) + "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 9daff4514617f7fd4d83f4228125a06651f501ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: gnu: r-wppi: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-wppi): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97181dbf06..645bdebf4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11856,13 +11856,13 @@ (define-public r-xcms (define-public r-wppi (package (name "r-wppi") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) + "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration -- cgit v1.2.3 From c7c004c36e7e4cf922c3847e210696ee67d8cf2d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-wrench: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 645bdebf4b..bdcb83bc04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11897,14 +11897,14 @@ (define-public r-wppi (define-public r-wrench (package (name "r-wrench") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) + "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 57fec18eae677e1aa0438e55ca37d2f99439ceba Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-wiggleplotr: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdcb83bc04..0f7a7eab59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11921,14 +11921,14 @@ (define-public r-wrench (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) + "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3")))) (build-system r-build-system) (propagated-inputs (list r-assertthat -- cgit v1.2.3 From 75ca7d19fd31ab1792c8bb1b433e3bff5819dc21 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-widgettools: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f7a7eab59..30fd93da0d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11955,14 +11955,14 @@ (define-public r-wiggleplotr (define-public r-widgettools (package (name "r-widgettools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) + "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") -- cgit v1.2.3 From 36edd2b28804fd1a892388e7f10de3a1763a1e41 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-webbioc: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30fd93da0d..9e99aae7c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11976,14 +11976,14 @@ (define-public r-widgettools (define-public r-webbioc (package (name "r-webbioc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) + "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2")))) (build-system r-build-system) (inputs (list netpbm perl)) -- cgit v1.2.3 From 70e32fd0bf7930d8401f85dfd067aec555d5daff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-zinbwave: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e99aae7c5..f94e78f725 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12008,14 +12008,14 @@ (define-public r-webbioc (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) + "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel -- cgit v1.2.3 From f16c7d46cc8830bd1ad6b51bb5e55e22750f5ed1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-zfpkm: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f94e78f725..8bec5700e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12041,14 +12041,14 @@ (define-public r-zinbwave (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) + "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 42e093c5759360bf2fc9123c9837348dfcdf8f8e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-rbowtie2: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8bec5700e6..c908d49091 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12066,14 +12066,14 @@ (define-public r-zfpkm (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) + "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 471040c5d10519aa8ab75cd092436d0f548915f5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-progeny: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c908d49091..31ff7db383 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12093,14 +12093,14 @@ (define-public r-rbowtie2 (define-public r-progeny (package (name "r-progeny") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) + "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 628ce9bf483fc51b813231cfaa21f5f64af0c290 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-arrmnormalization: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31ff7db383..51b9fd56ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12125,14 +12125,14 @@ (define-public r-progeny (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) + "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) -- cgit v1.2.3 From 43b69b74d3a133eca0e420d1942a05c4807e4e97 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-biocfilecache: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51b9fd56ec..6850503eca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12148,14 +12148,14 @@ (define-public r-arrmnormalization (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) + "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b35b27b983c9322d74977b0012c2cb86a0202b53 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-iclusterplus: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6850503eca..c9ed265aed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12181,14 +12181,14 @@ (define-public r-biocfilecache (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) + "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) -- cgit v1.2.3 From 0f6cd30c7af1c6f3c03bc629ad23b9983f00cb1b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-rbowtie: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c9ed265aed..f172d04b5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12211,14 +12211,14 @@ (define-public r-iclusterplus (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) + "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 41e534e93a0a840b5a0c42796379c98c31106050 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-sgseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f172d04b5c..feb15c43bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12247,14 +12247,14 @@ (define-public r-rbowtie (define-public r-sgseq (package (name "r-sgseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) + "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a9dd4f8bd61d39ad58ef0caa4b8d93db2c6e3c15 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: gnu: r-rhisat2: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index feb15c43bf..a1e370e707 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12290,14 +12290,14 @@ (define-public r-sgseq (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) + "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 1a99e38e8d0c53e4ff3679c42d16ba8d9a13f745 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-quasr: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1e370e707..66320d19ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12328,14 +12328,14 @@ (define-public r-rhisat2 (define-public r-quasr (package (name "r-quasr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) + "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From afd5dfff034394e20453672eea2c234aee87bd7f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-rqc: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66320d19ff..789a84badd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12370,14 +12370,14 @@ (define-public r-quasr (define-public r-rqc (package (name "r-rqc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) + "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From df921b1f69720544812c80f72e8570febd2fd735 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-birewire: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 789a84badd..a0370e8195 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12413,14 +12413,14 @@ (define-public r-rqc (define-public r-birewire (package (name "r-birewire") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) + "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 812fd22ad301e6b879f859197afa352da0951f9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-multidataset: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0370e8195..4cb52448f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12466,14 +12466,14 @@ (define-public r-birta (define-public r-multidataset (package (name "r-multidataset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) + "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8772941e80dc0b7ea83d5130d31c98e857226fdd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-ropls: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.30.0. [propagated-inputs]: Add r-plotly and r-ggplot2. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cb52448f1..b040ba8c89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12503,19 +12503,21 @@ (define-public r-multidataset (define-public r-ropls (package (name "r-ropls") - (version "1.28.2") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) + "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-ggplot2 r-multiassayexperiment r-multidataset + r-plotly r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes -- cgit v1.2.3 From 254acb7ddc298e6866c16adc835c152efae81677 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-biosigner: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b040ba8c89..78bf2fa352 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12545,14 +12545,14 @@ (define-public r-ropls (define-public r-biosigner (package (name "r-biosigner") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) + "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj")))) (build-system r-build-system) (propagated-inputs (list r-biobase -- cgit v1.2.3 From 2aaa3f4414447f15d1449b0d18852ac179a425c4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-annotatr: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78bf2fa352..8b19321453 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12580,14 +12580,14 @@ (define-public r-biosigner (define-public r-annotatr (package (name "r-annotatr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) + "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 9c3506a26cc462418421796e949bb69dc6aaa133 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-rsubread: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8b19321453..52207ab661 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12621,14 +12621,14 @@ (define-public r-annotatr (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.5") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) + "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 944e48a8611219d6e52692fa42581aa595bc6d19 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-consensusclusterplus: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52207ab661..7d42cdedaa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12673,14 +12673,14 @@ (define-public r-flowutils (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) + "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) -- cgit v1.2.3 From e6dc952cbb4ce8b942ff9ab5af6b9d50675ff686 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-cytolib: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d42cdedaa..6d18e5726a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12739,14 +12739,14 @@ (define-public r-cycombine (define-public r-cytolib (package (name "r-cytolib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) + "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From c5130dfef1f0668bf7bb79b4ec5347f56ad8396a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-flowcore: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.10.0. [propagated-inputs]: Remove r-rcpparmadillo; add r-cpp11. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d18e5726a..85cd44bf32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12768,24 +12768,24 @@ (define-public r-cytolib (define-public r-flowcore (package (name "r-flowcore") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) + "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-matrixstats r-rcpp - r-rcpparmadillo r-rprotobuflib r-s4vectors)) (native-inputs -- cgit v1.2.3 From 59a3f6df90eb9bd748f020a8018b0623dc40ea33 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-flowmeans: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85cd44bf32..873f139043 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12800,14 +12800,14 @@ (define-public r-flowcore (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) + "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a87bcca9f2bd9c8aa6a3754bd46292c75791df4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: gnu: r-ncdfflow: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 873f139043..850f2faca6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12823,14 +12823,14 @@ (define-public r-flowmeans (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7")))) + "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ffe3bfa1baea504f8de894553c0b7f3b5c0a0bec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-ggcyto: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 850f2faca6..f1a9549fab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12854,14 +12854,14 @@ (define-public r-ncdfflow (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325")))) + "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 22f8c5350e74686a84e1f1cb1000ad908faf7e04 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-flowviz: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1a9549fab..f1e9963cdd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12891,14 +12891,14 @@ (define-public r-ggcyto (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.2") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95")))) + "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 223fb324926f9c2cfe6a309000884a7b3a78de59 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-flowclust: Update to 3.36.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1e9963cdd..2d4e571a32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12922,14 +12922,14 @@ (define-public r-flowviz (define-public r-flowclust (package (name "r-flowclust") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) + "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From d029859dd293859d73684395ca06302a71251990 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-rprotobuflib: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d4e571a32..d1733c91ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12956,14 +12956,14 @@ (define-public r-flowclust (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) + "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 8a089e4e117183c3dd297bff70ae8f27a7775cbe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-flowworkspace: Update to 4.10.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d1733c91ff..3bea2eda02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12985,14 +12985,14 @@ (define-public r-rprotobuflib (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.8.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) + "07w2pnnzmivfc621c8pvndqrn1k245cwjrb0nnk2i85i3si4j9c3")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2061e5af92067bfeb7a5e7dbeb82d2490f00384d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-flowstats: Update to 4.10.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bea2eda02..2a922b19f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13039,14 +13039,14 @@ (define-public r-flowworkspace (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.2") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) + "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 522e1136b6b6ddb5bc2f8b4ca77c52f4f66ec73b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-opencyto: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a922b19f7..25c4257320 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13077,14 +13077,14 @@ (define-public r-flowstats (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) + "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 90be8abee62787cc5206c903c8460d97237bbf77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-cytoml: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25c4257320..5aee1f199f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13121,14 +13121,14 @@ (define-public r-opencyto (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) + "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 6741cfad7c0b2fdf927f440b295073da832cee09 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-flowsom: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5aee1f199f..36aa67ffef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13173,14 +13173,14 @@ (define-public r-cytoml (define-public r-flowsom (package (name "r-flowsom") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) + "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f80ad8d51bf8062f18c915a46e843e37069e4cc1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-mixomics: Update to 6.22.0. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36aa67ffef..35684c489d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13216,14 +13216,14 @@ (define-public r-flowsom (define-public r-mixomics (package (name "r-mixomics") - (version "6.20.0") + (version "6.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) + "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3073f30b07c207a8ab378e25186e593e2ede9a87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-depecher: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 35684c489d..83c3aff0d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13262,14 +13262,14 @@ (define-public r-mixomics (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) + "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3857d2dd8df4c33f8964fd8af26c83d749447eab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-rcistarget: Update to 1.17.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.17.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 83c3aff0d9..c61bf8ff6c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13308,14 +13308,14 @@ (define-public r-depecher (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.16.0") + (version "1.17.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) + "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 355400fff2cc2bdfc45fae3c1a966e20c1ca2f5b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: gnu: r-chicago: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-chicago): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c61bf8ff6c..1298fbe331 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13350,14 +13350,14 @@ (define-public r-rcistarget (define-public r-chicago (package (name "r-chicago") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) + "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5adc9823f847e471766db36caf8632351087ad70 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-cicero: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1298fbe331..4817a3ddd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13396,14 +13396,14 @@ (define-public r-ciara (define-public r-cicero (package (name "r-cicero") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) + "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat -- cgit v1.2.3 From a6580915af97f1f23239b1f74ce52a92853dd1f0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-circrnaprofiler: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4817a3ddd6..e75ae03698 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13463,14 +13463,14 @@ (define-public r-cicero-monocle3 (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) + "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) -- cgit v1.2.3 From f184b3a86bd6d9d7fd523af2e57e2bffe867bfe2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-genie3: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e75ae03698..0cda7ab027 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13598,14 +13598,14 @@ (define-public r-cistopic-next (define-public r-genie3 (package (name "r-genie3") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) + "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d29b13e9be0485b7904417a8e6148ec36be4d981 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-roc: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0cda7ab027..2bb4cc0497 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13622,14 +13622,14 @@ (define-public r-genie3 (define-public r-roc (package (name "r-roc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) + "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 1d03230dc856af37553b91e309d58a58966289bf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-watermelon: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bb4cc0497..546f87a2ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13644,14 +13644,14 @@ (define-public r-roc (define-public r-watermelon (package (name "r-watermelon") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) + "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ba535c8148a37e4c52e2374b7250bda024c139f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-gdsfmt: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 546f87a2ce..08f4549f29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13682,14 +13682,14 @@ (define-public r-watermelon (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) + "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. -- cgit v1.2.3 From 63b8d104dc0bfa88553887ca6961ffcf08043eab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-bigmelon: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08f4549f29..79f601d02c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13738,14 +13738,14 @@ (define-public r-gdsfmt (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) + "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1f7c82bf0b1d840b34d1ee6b1aaf447cecff9899 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-seqbias: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79f601d02c..0110db4a81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13769,14 +13769,14 @@ (define-public r-bigmelon (define-public r-seqbias (package (name "r-seqbias") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) + "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d9b593d522ca85fc9bae0c1b1fe9572ae2e47f3a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-reqon: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0110db4a81..bd25da0fe5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13793,14 +13793,14 @@ (define-public r-seqbias (define-public r-reqon (package (name "r-reqon") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) + "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 827abdb960cb59d78527d257ab7ddac43d20cd6e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-wavcluster: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd25da0fe5..a46a78fc54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13816,14 +13816,14 @@ (define-public r-reqon (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) + "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8a2f4b7192d095f1d921dd4141bf1a486fc27d2d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-variantfiltering: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a46a78fc54..f5ba721d51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13904,14 +13904,14 @@ (define-public r-timeseriesexperiment (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) + "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) -- cgit v1.2.3 From 30bfeccabb217f13bb02f6aacd564f65992609ca Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-variancepartition: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5ba721d51..60010c26a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14010,14 +14010,14 @@ (define-public r-wavetiling (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) + "1mn91r0yrhz08m3vs2h3i35rcbxyc7sdfknmk6vcw1z75znjsnpl")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) -- cgit v1.2.3 From 86eddd9e14f9a5b8e05ba4dc7a1f48fa55456449 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-htqpcr: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60010c26a9..e1fef9c109 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14058,14 +14058,14 @@ (define-public r-variancepartition (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) + "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ba16a0a2ee0a4cc49dbda64fe18bebee27f31a66 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: gnu: r-unifiedwmwqpcr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e1fef9c109..a6205fe08c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14088,14 +14088,14 @@ (define-public r-htqpcr (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) + "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) -- cgit v1.2.3 From ffea168d764ae7de55c6d12f4f4a29bc40239e75 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-universalmotif: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6205fe08c..a6d7576666 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14112,14 +14112,14 @@ (define-public r-unifiedwmwqpcr (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr")))) + "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) -- cgit v1.2.3 From 949b5f3ddb7443b042970ebdd759cb5b250cda15 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-ace: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-ace): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6d7576666..aea93d74fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14160,13 +14160,13 @@ (define-public r-universalmotif (define-public r-ace (package (name "r-ace") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) + "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) -- cgit v1.2.3 From b5a0834c2f0c4012dcd26878f8eeb0af8a8a5d78 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-acgh: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-acgh): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aea93d74fc..86218db20d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14189,13 +14189,13 @@ (define-public r-ace (define-public r-acgh (package (name "r-acgh") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) + "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) -- cgit v1.2.3 From 5fed6cbcbce444673c48d1bf21fdb3aaf363a1d6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-acme: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-acme): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86218db20d..f545059e82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14213,13 +14213,13 @@ (define-public r-acgh (define-public r-acme (package (name "r-acme") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) + "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) -- cgit v1.2.3 From fcde82ae09852caed0676b46843c5bbbf6815e4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-acde: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-acde): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f545059e82..3c828535c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14240,13 +14240,13 @@ (define-public r-acme (define-public r-acde (package (name "r-acde") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) + "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) -- cgit v1.2.3 From ade1bef97a75dda2e76ffaac260a15e9492ca3c9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-bgmix: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3c828535c1..b256de0da6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14333,14 +14333,14 @@ (define-public r-activepathways (define-public r-bgmix (package (name "r-bgmix") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) + "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 16e636eccb3d276ffdfc61f131ff8bffbd4f65bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-bgx: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b256de0da6..03c256705e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14355,14 +14355,14 @@ (define-public r-bgmix (define-public r-bgx (package (name "r-bgx") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) + "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 02928ed15f030c3600489e18564eb82c01a5af14 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-bhc: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03c256705e..979ffdf4f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14391,14 +14391,14 @@ (define-public r-bgx (define-public r-bhc (package (name "r-bhc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) + "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") -- cgit v1.2.3 From 002ef09276b26a760242bf6ecbd32b24b1f7442b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-bicare: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 979ffdf4f5..c47103cb21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14417,14 +14417,14 @@ (define-public r-bhc (define-public r-bicare (package (name "r-bicare") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) + "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a1d8a95a0671be70d70ff8cf64f61b922ce0ae6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-bifet: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c47103cb21..b39ab8f9bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14439,14 +14439,14 @@ (define-public r-bicare (define-public r-bifet (package (name "r-bifet") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) + "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4665e589d676a551022a8072e6dabee90e5c1ac1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-rsbml: Update to 2.56.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b39ab8f9bd..e50395ad62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14468,14 +14468,14 @@ (define-public r-bifet (define-public r-rsbml (package (name "r-rsbml") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) + "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 7939489f80196e5cd9797e7a8ff3066dcc0f992f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-hypergraph: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e50395ad62..e332bcfdf3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14494,14 +14494,14 @@ (define-public r-rsbml (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) + "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b90e4cdd5623964cbfcb74cc386bf6c04de4ecc3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-hyperdraw: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e332bcfdf3..fe78204e26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14516,14 +14516,14 @@ (define-public r-hypergraph (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) + "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) -- cgit v1.2.3 From dae60e1c1f38a2d7f49eff3021c60d3acd2771b1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: gnu: r-biggr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe78204e26..d0a006ed29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14538,14 +14538,14 @@ (define-public r-hyperdraw (define-public r-biggr (package (name "r-biggr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) + "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 087322f6fa5a70fb4b397b0465e653cf31ad81ea Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-bigpint: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0a006ed29..b2118bc042 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14602,14 +14602,14 @@ (define-public r-bigmemoryextras (define-public r-bigpint (package (name "r-bigpint") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) + "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8bbcb000c720249f86e15975bede563cd39a155f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-chemminer: Update to 3.50.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2118bc042..28c1d0a74a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14645,14 +14645,14 @@ (define-public r-bigpint (define-public r-chemminer (package (name "r-chemminer") - (version "3.48.0") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) + "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4cf44682fb35e17f365f392a11c7301c7582cf4c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-fmcsr: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-fmcsr): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28c1d0a74a..000f69c2f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14688,13 +14688,13 @@ (define-public r-chemminer (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) + (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a6a6f4466fc0f25a0d7709863a0e539c5d8a4d0a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-bioassayr: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 000f69c2f6..1de08e3630 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14717,14 +14717,14 @@ (define-public r-fmcsr (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) + "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 828084b2cb3228c3af79b435d3d09d6e64a9127a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-biobroom: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1de08e3630..272d1b3bb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14752,14 +14752,14 @@ (define-public r-bioassayr (define-public r-biobroom (package (name "r-biobroom") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) + "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2cd3b140710b501d540a43fbf9968117302bdb55 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-graphite: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.44.0. [propagated-inputs]: Add r-purrr. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 272d1b3bb3..1f8857d38a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14781,18 +14781,18 @@ (define-public r-biobroom (define-public r-graphite (package (name "r-graphite") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) + "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) + (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description -- cgit v1.2.3 From 0f7ac7b091cd2b14b600e5774feefb39f565f24e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-reactomepa: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.42.0. [propagated-inputs]: Add r-gson. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f8857d38a..c33bfa4d53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14804,14 +14804,14 @@ (define-public r-graphite (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) + "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -14821,6 +14821,7 @@ (define-public r-reactomepa r-ggplot2 r-ggraph r-graphite + r-gson r-igraph r-reactome-db)) (native-inputs -- cgit v1.2.3 From 712bce2124b7ece8bdd315c3ea85c846d1a7dfde Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-ebarrays: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c33bfa4d53..cffb708e9b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14837,14 +14837,14 @@ (define-public r-reactomepa (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) + "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5f39d8aa867dfc293533541dd70c91b7629ee3dd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-bioccheck: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cffb708e9b..94a95a6ec9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14903,13 +14903,13 @@ (define-public r-bioccasestudies (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw")))) + "0ncvxqx3irc7nv9ib93kz1c3lxyqc4y6g0g11ymxrqx7i4g3qgb8")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From dfad35abc698394cf2a04b42306790270a5168eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-biocgraph: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 94a95a6ec9..abbf55e892 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14932,14 +14932,14 @@ (define-public r-bioccheck (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) + "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dcb59af845473041eccba43a43a2b51638e9b3bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-biocstyle: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index abbf55e892..29a864fb93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14954,13 +14954,13 @@ (define-public r-biocgraph (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) + "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From d87f979e28f39176f5647949099362b96f8b56e6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-biocviews: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29a864fb93..84840fc9fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14978,13 +14978,13 @@ (define-public r-biocstyle (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38")))) + "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 97629088897c202ae1c0f481ddf16a3ad24a79ae Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: gnu: r-experimenthub: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84840fc9fc..dd2e2bcd9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15006,14 +15006,14 @@ (define-public r-biocviews (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) + "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 55c39e29470806a1e062e557a54714f0b0796bb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-grohmm: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-grohmm): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd2e2bcd9e..31a8b9925f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15040,14 +15040,14 @@ (define-public r-experimenthub (define-public r-grohmm (package (name "r-grohmm") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) + "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5557dea898f63d2165004692377e5b36f6dc1a46 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-multiassayexperiment: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.24.0. [propagated-inputs]: Add r-biocbaseutils and r-delayedarray. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31a8b9925f..678ffb128e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15067,20 +15067,22 @@ (define-public r-grohmm (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) + "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-biocbaseutils r-biocgenerics + r-delayedarray r-genomicranges r-iranges r-s4vectors -- cgit v1.2.3 From 1eaf500dd684337e4a4f6c2c5d8239cd9bc943fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-bioconcotk: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 678ffb128e..fbca4b0040 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15104,14 +15104,14 @@ (define-public r-multiassayexperiment (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) + "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1a19353ae1dac0b08540bd9883ae0e16e1e23825 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-biocor: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbca4b0040..22c62534d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15149,14 +15149,14 @@ (define-public r-bioconcotk (define-public r-biocor (package (name "r-biocor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) + "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c1cff36f4c30a3d8a903eeb5b02191a76786e0ed Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-biocpkgtools: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.16.0. [propagated-inputs]: Remove r-tidyr and r-tidyselect. Add r-rorcid. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22c62534d9..4f9838e875 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15176,14 +15176,14 @@ (define-public r-biocor (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd")))) + "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -15203,11 +15203,10 @@ (define-public r-biocpkgtools r-rbgl r-readr r-rlang + r-rorcid r-rvest r-stringr r-tibble - r-tidyr - r-tidyselect r-xml2)) (native-inputs (list r-knitr)) -- cgit v1.2.3 From ec4583b1d203a2139d98b6198f6cbdd3a789e9fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-biocset: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f9838e875..619b6721fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15223,14 +15223,14 @@ (define-public r-biocpkgtools (define-public r-biocset (package (name "r-biocset") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) + "197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3e451b9415528732582087c7d9875accfd54ae5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-biocworkflowtools: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 619b6721fa..7c6f950a5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15261,14 +15261,14 @@ (define-public r-biocset (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) + "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) -- cgit v1.2.3 From 29c12faa8736af26c9d20492b2bc734c2a1f6a7c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-biodist: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c6f950a5f..1e56317e8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15294,14 +15294,14 @@ (define-public r-biocworkflowtools (define-public r-biodist (package (name "r-biodist") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) + "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4f3b6abb5f1b2763bbc7917767aee357949c2a3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-pcatools: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e56317e8a..f4daeb867d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15316,14 +15316,14 @@ (define-public r-biodist (define-public r-pcatools (package (name "r-pcatools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) + "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c705fcaaa5800f5dc781898fee5d017568a488cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-rgreat: Update to 2.0.1. * gnu/packages/bioconductor.scm (r-rgreat): Update to 2.0.1. [propagated-inputs]: Add r-annotationdbi, r-circlize, r-digest, r-doparallel, r-dt, r-foreach, r-genomeinfodb, r-genomicfeatures, r-globaloptions, r-go-db, r-org-hs-eg-db, r-progress, r-rcolorbrewer, r-rcpp, r-s4vectors, r-shiny, r-txdb-hsapiens-ucsc-hg19-knowngene, and r-txdb-hsapiens-ucsc-hg38-knowngene. --- gnu/packages/bioconductor.scm | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f4daeb867d..71a060be87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15362,18 +15362,40 @@ (define-public r-pcatools (define-public r-rgreat (package (name "r-rgreat") - (version "1.28.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) + "1s1xx15ilamcyd8f7cnsgdc3r3izhx9wxmb8amamrmr9bzijjvhi")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (list r-annotationdbi + r-circlize + r-digest + r-doparallel + r-dt + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-getoptlong + r-globaloptions + r-go-db + r-iranges + r-org-hs-eg-db + r-progress + r-rcolorbrewer + r-rcurl + r-rcpp + r-rjson + r-s4vectors + r-shiny + r-txdb-hsapiens-ucsc-hg19-knowngene + r-txdb-hsapiens-ucsc-hg38-knowngene)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") -- cgit v1.2.3 From 79c096cb2e88ef386f62ac078c849faa645d2e6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-m3c: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71a060be87..55d34f2a6e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15408,14 +15408,14 @@ (define-public r-rgreat (define-public r-m3c (package (name "r-m3c") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) + "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a02007bd88bf00dbcdad098d4a0acd4da864d938 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: gnu: r-icens: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d34f2a6e..9f6d794e9c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15441,14 +15441,14 @@ (define-public r-m3c (define-public r-icens (package (name "r-icens") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) + "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4737a25691f7f845200ffda1ef3caa4d25f0ba5c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-preprocesscore: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f6d794e9c..158de128a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15564,14 +15564,14 @@ (define-public r-fourcseq (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) + "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit v1.2.3 From 96cd3b4bcff89fd8317505fb29505ec6f8119e9e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-s4vectors: Update to 0.36.0. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 158de128a1..58baa4dd3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15585,13 +15585,13 @@ (define-public r-preprocesscore (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) + "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From f074346f2cfd4b97329e24c811c050d390c4c886 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-rgraphviz: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58baa4dd3a..e915145f7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15652,14 +15652,14 @@ (define-public r-wgcna (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) + "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 65866be416001593588d9e1d2c49f0a3267ad80c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-fishpond: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-fishpond): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e915145f7e..7b9f814a19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15690,13 +15690,13 @@ (define-public r-rgraphviz (define-public r-fishpond (package (name "r-fishpond") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 06c18fde52f9e9e211420758af94f2d3ccab966f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-fithic: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b9f814a19..bc58bea7d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15728,13 +15728,13 @@ (define-public r-fishpond (define-public r-fithic (package (name "r-fithic") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) + "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ab92277de4c5ff4622558feffb9627643883a450 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-hitc: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc58bea7d7..a90766ee19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15752,13 +15752,13 @@ (define-public r-fithic (define-public r-hitc (package (name "r-hitc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) + "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9e45f2c18346d2dec417919312c029b2c49f7caf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-hdf5array: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a90766ee19..e13009209b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15781,14 +15781,14 @@ (define-public r-hitc (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9")))) + "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 2a5fb31db95c02741b36c290241463723accda92 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-rhdf5lib: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e13009209b..08d853dcdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15812,14 +15812,14 @@ (define-public r-hdf5array (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) + "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 6dfa3f50b9286fee202a594f9c1284f575b5bde4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-beachmat: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08d853dcdf..fa706304c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15892,14 +15892,14 @@ (define-public r-rhdf5lib (define-public r-beachmat (package (name "r-beachmat") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) + "0sa1wh997jfiz2y0dr7v12b7pvlf7icgv6arlyqy57winbnqa96m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) -- cgit v1.2.3 From 6dc8ec03589d208fa4ab1686872c3cd3361a2293 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-cner: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-cner): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa706304c6..a8ca442cd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15918,13 +15918,13 @@ (define-public r-beachmat (define-public r-cner (package (name "r-cner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) + (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 21b32e45bd3e32d9f729441f11b2f2bb67d7c1ab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-tfbstools: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8ca442cd6..0e9e11295b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15966,14 +15966,14 @@ (define-public r-cner (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) + "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8b332d676d06188f6dfb200099def4220106a7a3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-maftools: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-maftools): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e9e11295b..76d3b57d04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16012,13 +16012,13 @@ (define-public r-tfbstools (define-public r-maftools (package (name "r-maftools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) + (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5374b55b68ad5713f97e2fc30ebcde73be00ce5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-motifmatchr: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76d3b57d04..d6b1836449 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16041,14 +16041,14 @@ (define-public r-maftools (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) + "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 64ccd0ff3cbf23ef05ae031456434eb8dbca41eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: gnu: r-chromvar: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d6b1836449..f9ea235018 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16075,13 +16075,13 @@ (define-public r-motifmatchr (define-public r-chromvar (package (name "r-chromvar") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) + (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d748ae3d00039d9747cf3f54c2e2a950ab8031b8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-singlecellexperiment: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9ea235018..45d831bdfc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16122,14 +16122,14 @@ (define-public r-chromvar (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) + "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 54a67ddf86e7dcd8769c9fa01e62c2df39e040c2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-singler: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-singler): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45d831bdfc..501628ff93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16150,13 +16150,13 @@ (define-public r-singlecellexperiment (define-public r-singler (package (name "r-singler") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) + (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3fa18b550480ca4b8b3d63e9eef8c4f601a4ff81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-scuttle: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 501628ff93..d73de67236 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16182,14 +16182,14 @@ (define-public r-singler (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671")))) + "1z9pigcqfqyp5n6n9gbmw3ix4f1v0ayxi4xmxj7c4d0vdm5c8c2s")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 14e3905c6e5c4a3d4b56b22488e4f8a6ff88f537 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-scater: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-scater): Update to 1.26.1. [propagated-inputs]: Add r-ggrastr, r-pheatmap, and r-uwot. --- gnu/packages/bioconductor.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d73de67236..cbb9123595 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16217,13 +16217,13 @@ (define-public r-scuttle (define-public r-scater (package (name "r-scater") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) + "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -16236,8 +16236,10 @@ (define-public r-scater r-ggbeeswarm r-ggplot2 r-ggrepel + r-ggrastr r-gridextra r-matrix + r-pheatmap r-rcolorbrewer r-rcppml r-rlang @@ -16246,6 +16248,7 @@ (define-public r-scater r-scuttle r-singlecellexperiment r-summarizedexperiment + r-uwot r-viridis)) (native-inputs (list r-knitr)) -- cgit v1.2.3 From c73d3e9bad9f1c21b4cda6f827a2e3eaec001e48 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-scran: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-scran): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cbb9123595..b565f83f55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16262,14 +16262,14 @@ (define-public r-scater (define-public r-scran (package (name "r-scran") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni")))) + "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) (build-system r-build-system) (propagated-inputs (list r-beachmat -- cgit v1.2.3 From 2dc26068eba6de2133b4b8fd71e65bfb30a6fd9a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-sparsematrixstats: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b565f83f55..d2faf65077 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16305,14 +16305,14 @@ (define-public r-scran (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) + "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From 377a9b2177cdd7a1e614b6aade1cf34fdec9302c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2faf65077..2a0e2db1d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16330,14 +16330,14 @@ (define-public r-sparsematrixstats (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv")))) + "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From b5a0d814489534ad3bee09703480846c6a729e67 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-mscoreutils: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a0e2db1d1..4cfaa23442 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16366,14 +16366,14 @@ (define-public r-delayedmatrixstats (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) + "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0640f750b425b2cacc3f8609bbf953c702f00739 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-msfeatures: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cfaa23442..7230882fa7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16395,13 +16395,13 @@ (define-public r-mscoreutils (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) + (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 94a86e7e39c7db7ee75d780b29865bee47b09fff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-biocio: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocio): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7230882fa7..ac0023a9be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16425,14 +16425,14 @@ (define-public r-msfeatures (define-public r-biocio (package (name "r-biocio") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) + "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5c6c7831d62b4160dcf34a953acb74321f245176 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-msmseda: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-msmseda): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac0023a9be..2e6ae69fe4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16458,14 +16458,14 @@ (define-public r-biocio (define-public r-msmseda (package (name "r-msmseda") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) + "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 01e78296bc3286f0ed3322c726fce31d0c64f2ce Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-msmstests: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-msmstests): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e6ae69fe4..c8159010a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16481,14 +16481,14 @@ (define-public r-msmseda (define-public r-msmstests (package (name "r-msmstests") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) + "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dbeb05e6a3bbe2eaeb62b8198b2d8c3464235ad8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: gnu: r-catalyst: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-catalyst): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8159010a2..39898e97a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16510,14 +16510,14 @@ (define-public r-msmstests (define-public r-catalyst (package (name "r-catalyst") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) + "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 77f2aa3fa4dae5329f3bba522d0f328b828b9084 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-erma: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-erma): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39898e97a4..15eab6a923 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16573,14 +16573,14 @@ (define-public r-catalyst (define-public r-erma (package (name "r-erma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) + "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From 34867ac9cf0d5a882b3a70223df51c7317b3737d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-ggbio: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15eab6a923..3558a37ad3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16613,14 +16613,14 @@ (define-public r-erma (define-public r-ggbio (package (name "r-ggbio") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg")))) + "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 5f3ff4f884f83455fbc25c291cf482da7245bf81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-gviz: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3558a37ad3..d9e0e4e14a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16781,14 +16781,14 @@ (define-public r-gqtlstats (define-public r-gviz (package (name "r-gviz") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) + "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b6e56ceeb990a417b9a88118ed0c4021de6ffb1f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-gwascat: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-gwascat): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9e0e4e14a..c62bb4fe2c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16830,14 +16830,14 @@ (define-public r-gviz (define-public r-gwascat (package (name "r-gwascat") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) + "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi -- cgit v1.2.3 From db290bf5b991cf9d7b34b3699c211fdb748a94df Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-kegggraph: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62bb4fe2c..0fcced71a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16864,13 +16864,13 @@ (define-public r-gwascat (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) + (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1315c532de6850f983bb83163f021012995224b8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-ldblock: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-ldblock): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fcced71a4..7a736fdc3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16888,14 +16888,14 @@ (define-public r-kegggraph (define-public r-ldblock (package (name "r-ldblock") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) + "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics -- cgit v1.2.3 From ddc7edf0b3ec4f7a7dba863364592b2180315f39 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-pathview: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a736fdc3c..1e76ac9158 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17012,13 +17012,13 @@ (define-public r-spp (define-public r-pathview (package (name "r-pathview") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71")))) + (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1ff0bc4e7b4685d13c2e3c6603a80410ef94e483 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-snpstats: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-snpstats): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e76ac9158..d7d0ca6920 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17046,14 +17046,14 @@ (define-public r-pathview (define-public r-snpstats (package (name "r-snpstats") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) + "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 5950a171ba9f89b918d2fc4c842855ee381c3e7c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-chromstar: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-chromstar): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d7d0ca6920..6f9b5dcee9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17070,14 +17070,14 @@ (define-public r-snpstats (define-public r-chromstar (package (name "r-chromstar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) + "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3ca58a4ff35e06487d55810fd8222e90ce359869 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-guitar: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-guitar): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f9b5dcee9..69b722c8b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17108,14 +17108,14 @@ (define-public r-chromstar (define-public r-guitar (package (name "r-guitar") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) + "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3823aa40a34426e7d9c07ab1e9b75290765a0c5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-ballgown: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-ballgown): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69b722c8b6..7af742b3f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17161,14 +17161,14 @@ (define-public r-sushi (define-public r-ballgown (package (name "r-ballgown") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) + "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5604f64c342b04f6e8f06cad6fca15d6108d72c6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-megadepth: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-megadepth): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7af742b3f6..aba0a43e1d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17195,14 +17195,14 @@ (define-public r-ballgown (define-public r-megadepth (package (name "r-megadepth") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) + "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) -- cgit v1.2.3 From 81cea8424d8ca7a9189b3920b83cb5e34a75716e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: gnu: r-beclear: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-beclear): Update to 2.14.0. [propagated-inputs]: Add r-ids. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aba0a43e1d..5536954335 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17228,14 +17228,14 @@ (define-public r-megadepth (define-public r-beclear (package (name "r-beclear") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) + "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -17244,6 +17244,7 @@ (define-public r-beclear r-data-table r-dixontest r-futile-logger + r-ids r-matrix r-rcpp r-rdpack)) -- cgit v1.2.3 From 3912f43996883094a30ba28d1c3b24f716cc9f8b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-bgeecall: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5536954335..cba1d09841 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17262,14 +17262,14 @@ (define-public r-beclear (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil")))) + "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 009ac4e3a93475e2665d18cc4ee5c5b8ab898975 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-bgeedb: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cba1d09841..7afc365b04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17298,14 +17298,14 @@ (define-public r-bgeecall (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.22.3") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k")))) + "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8ba466faff5154a879dffc9fd0ea63af7ddbf2f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biobtreer: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7afc365b04..635ca45724 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17332,14 +17332,14 @@ (define-public r-bgeedb (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) + "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dbaad2365aa0899522965725cd82b55ad7006bf5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-minet: Update to 3.56.0. * gnu/packages/bioconductor.scm (r-minet): Update to 3.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 635ca45724..9724e94075 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17356,14 +17356,14 @@ (define-public r-biobtreer (define-public r-minet (package (name "r-minet") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) + "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 727cd07d1a6f69d9f8846c9e43a5e5587e3bd1eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-genetclassifier: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9724e94075..3b03612045 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17378,14 +17378,14 @@ (define-public r-minet (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) + "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) -- cgit v1.2.3 From 925642f837a5c9d4fc7ce45dc715e6a7ca7453d4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-dir-expiry: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3b03612045..b348f15405 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17403,14 +17403,14 @@ (define-public r-genetclassifier (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) + "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) -- cgit v1.2.3 From f5a514b60576a87821fbf2389b2550f05c95dd27 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-basilisk-utils: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b348f15405..3218e3fc32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17427,14 +17427,14 @@ (define-public r-dir-expiry (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) + "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) -- cgit v1.2.3 From 3aea2c40d8caafdf032a5a51b59173d7b25c2cfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-basilisk: Update to 1.10.2. * gnu/packages/bioconductor.scm (r-basilisk): Update to 1.10.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3218e3fc32..a96ade0f14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17451,14 +17451,14 @@ (define-public r-basilisk-utils (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk")))) + "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4fcf1f08ec9a34beab41018ba577903a7549fba8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biocthis: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-biocthis): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a96ade0f14..eef6919fda 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17477,14 +17477,14 @@ (define-public r-basilisk (define-public r-biocthis (package (name "r-biocthis") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) + "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From efc663040bc6a8eadc7856713aa306afaf04488e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biocdockermanager: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eef6919fda..f5666b0005 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17511,14 +17511,14 @@ (define-public r-biocthis (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d")))) + "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) -- cgit v1.2.3 From ffd5e53e8729702c6db237817df1a2c7da24c20b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biodb: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5666b0005..0c62f98bf9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17541,14 +17541,14 @@ (define-public r-biocdockermanager (define-public r-biodb (package (name "r-biodb") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1")))) + "08ahz3v2xbhwfh89dbnhhcdm0x5qv4hibi8wknlqf5x8gqm5j5w6")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4875f37cb6a8a5f2203cbad943d517b512546a59 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biomformat: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biomformat): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c62f98bf9..40d7a65608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17586,14 +17586,14 @@ (define-public r-biodb (define-public r-biomformat (package (name "r-biomformat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) + "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3879ddbdb98bf65a1593756301629e7ef38eaa34 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-mvcclass: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40d7a65608..301aadeb73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17615,14 +17615,14 @@ (define-public r-biomformat (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) + "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") -- cgit v1.2.3 From c0412736d88cd7ef5d0f848aefba3255fa7ab760 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: gnu: r-biomvcclass: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 301aadeb73..ca40129dff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17635,14 +17635,14 @@ (define-public r-mvcclass (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) + "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 858d9ccd9bb38be880f64cad603c4a201931feed Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-biomvrcns: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca40129dff..af9b15f5a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17657,14 +17657,14 @@ (define-public r-biomvcclass (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) + "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1118d6e85672e7335d4dfa88c71832d4aa308571 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-bionero: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-bionero): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af9b15f5a9..597618fb7c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17682,14 +17682,14 @@ (define-public r-biomvrcns (define-public r-bionero (package (name "r-bionero") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp")))) + "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 01fb7c35e7580bd8b015c073476a6724f25c7a18 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-bionet: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bionet): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 597618fb7c..47a4cd5c60 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17738,14 +17738,14 @@ (define-public r-bionero (define-public r-bionet (package (name "r-bionet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) + "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 219b98fee9402ac9810198ecfb281c8cfb448ca4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-bionetstat: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47a4cd5c60..c1f29ab421 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17767,14 +17767,14 @@ (define-public r-bionet (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2")))) + "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f230df5f4fac80460ff1b6298af2608646c7e377 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-bioqc: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-bioqc): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1f29ab421..c39f5ecba6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17809,14 +17809,14 @@ (define-public r-bionetstat (define-public r-bioqc (package (name "r-bioqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) + "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3ed0a63106cbe2ad5f4406b115da73afbd5e1489 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-biotip: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biotip): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c39f5ecba6..ea2e1fec58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17835,14 +17835,14 @@ (define-public r-bioqc (define-public r-biotip (package (name "r-biotip") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) + "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3b8df103f725332c0409c5beb856391558133019 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-biotmle: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biotmle): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea2e1fec58..857ede1403 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17865,14 +17865,14 @@ (define-public r-biotip (define-public r-biotmle (package (name "r-biotmle") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) + "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c2c91d9dfe9b767f3a808aaefd87c3f31a808383 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-bsseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bsseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 857ede1403..752662fb93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17907,14 +17907,14 @@ (define-public r-biotmle (define-public r-bsseq (package (name "r-bsseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) + "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95792cda899aeb69c5c0952fa05bfa47bd5d0f11 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-dada2: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-dada2): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 752662fb93..72f5ccb6e1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17953,13 +17953,13 @@ (define-public r-bsseq (define-public r-dada2 (package (name "r-dada2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e524c12e063eac2b560b6f7b6216ae6edca59dda Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-dmrseq: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72f5ccb6e1..a2bb6b33d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17990,14 +17990,14 @@ (define-public r-dada2 (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) + "1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3f5845473954dddfea7c9343e7bd97cde4b223c0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-omicade4: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-omicade4): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a2bb6b33d5..687fc4cbb7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18036,13 +18036,13 @@ (define-public r-dmrseq (define-public r-omicade4 (package (name "r-omicade4") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj")))) + "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) -- cgit v1.2.3 From 926fe78f73bbde29b9311cc5363f18a6c6719c5d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-omnipathr: Update to 3.5.25. * gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.5.25. [propagated-inputs]: Add r-rmarkdown and r-rvest. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 687fc4cbb7..5032eb8a91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18055,13 +18055,13 @@ (define-public r-omicade4 (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.4.0") + (version "3.5.25") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) + (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -18081,12 +18081,14 @@ (define-public r-omnipathr r-later r-logger r-magrittr + r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang + r-rvest r-stringr r-tibble r-tidyr -- cgit v1.2.3 From dde0da5a950e171853fb0e9a71c2b35cb27ca8d3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: gnu: r-biscuiteer: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5032eb8a91..246ac591c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18110,14 +18110,14 @@ (define-public r-omnipathr (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) + "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7a33311bfdd4030cc0ce32f713cd52c512b5d9f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: gnu: r-tcgabiolinks: Update to 2.25.3. * gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.25.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 246ac591c8..e4a235edad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18162,13 +18162,13 @@ (define-public r-biscuiteer (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.24.3") + (version "2.25.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms")))) + (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5140be4c8147615495ac99bfb1f6f64a2065757d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: gnu: r-tricycle: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-tricycle): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4a235edad..15c408185e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18217,13 +18217,13 @@ (define-public r-tcgabiolinks (define-public r-tricycle (package (name "r-tricycle") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) + "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9988c60ea31991ec841a205d1d44153235b1b5cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: gnu: r-tximeta: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15c408185e..aa47ce0a2e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18256,14 +18256,14 @@ (define-public r-tricycle (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8")))) + "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 54afdb3de18f4a0665ebfc451f788be9a553bd82 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: gnu: r-phyloseq: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa47ce0a2e..1b1a007c1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18297,13 +18297,13 @@ (define-public r-tximeta (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) + (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 04340b27bae6355b90c7bdf3f3d39c99bc0d03ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:16 +0100 Subject: gnu: r-bambu: Update to 3.0.2. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b1a007c1b..ac1876afa0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2923,13 +2923,13 @@ (define-public r-badregionfinder (define-public r-bambu (package (name "r-bambu") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "08vh0vbmjn1kzp10yrinn0p0ab2cjhgiagx1vhci5sf4s6p20vy4")))) + "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d3696e71a985930b54f0dbbd2722cb0a6530cf96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: gnu: r-deconvr: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac1876afa0..19924b3f77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3507,13 +3507,13 @@ (define-public r-decontam (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "14cxrcv5q6w20bq2pbxj75c0lzz96dxwqh1hqh2cl8nvvfi70jsv")))) + "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3bc54ddeab1e5a28d4844ab8c5441155ca205381 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: gnu: r-chipseeker: Update to 1.34.1. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.34.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19924b3f77..9466dbc130 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4772,13 +4772,13 @@ (define-public r-category (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1s90q73lldnmh2nxyb36hv44s3pj2l7pr0qka0z27b3cmnhqh50z")))) + "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From a5ee462b7a3d014abb21c9a00969bb2989b0eaef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: gnu: r-shortread: Update to 1.56.1. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.56.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9466dbc130..e308b9041d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6936,14 +6936,14 @@ (define-public r-seqpattern (define-public r-shortread (package (name "r-shortread") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0z700mjll3zv3451rd6p5195w0g3rmw17xddc5qwflwm8dnhdmll")))) + "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From f9747ecc2c81fcec187d0a0f81dba2bbdb4a8410 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: gnu: r-dose: Update to 3.24.2. * gnu/packages/bioconductor.scm (r-dose): Update to 3.24.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e308b9041d..6d2b9f9021 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10463,14 +10463,14 @@ (define-public r-fgsea (define-public r-dose (package (name "r-dose") - (version "3.24.1") + (version "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1ai42pnd8s8ws6y9nlq5d858w2rp8gfw2vpndslspj4q8gc4dbb1")))) + "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8bfac375aa5f28d14e99faa1e8a19119cae576ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: gnu: r-bioccheck: Update to 1.34.2. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.34.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d2b9f9021..bca34e2cdc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14903,13 +14903,13 @@ (define-public r-bioccasestudies (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0ncvxqx3irc7nv9ib93kz1c3lxyqc4y6g0g11ymxrqx7i4g3qgb8")))) + "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From a2ad5b53bfc660a8ca4a44f307f2eed1bcdb9fcf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: gnu: r-rgreat: Update to 2.0.2. * gnu/packages/bioconductor.scm (r-rgreat): Update to 2.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bca34e2cdc..dd9405affc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15362,14 +15362,14 @@ (define-public r-pcatools (define-public r-rgreat (package (name "r-rgreat") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "1s1xx15ilamcyd8f7cnsgdc3r3izhx9wxmb8amamrmr9bzijjvhi")))) + "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f43a41d1966638b0b75a46276c76642cb89e3023 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: gnu: r-scuttle: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd9405affc..19b17651b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16182,14 +16182,14 @@ (define-public r-singler (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1z9pigcqfqyp5n6n9gbmw3ix4f1v0ayxi4xmxj7c4d0vdm5c8c2s")))) + "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 13e8930efb855f3332045f38b558fecab50ac7fa Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 20 Jun 2022 00:33:46 +0200 Subject: gnu: Add r-arrayexpress. * gnu/packages/bioconductor.scm (r-arrayexpress): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19b17651b2..da7420d9f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2472,6 +2472,31 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayexpress + (package + (name "r-arrayexpress") + (version "1.56.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ArrayExpress" version)) + (sha256 + (base32 + "0v2v7v0gim0bsg34ciplapz6mjih68yqhcgzdlhcyj2d6vrgiad5")))) + (properties `((upstream-name . "ArrayExpress"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-limma + r-oligo + r-xml)) + (home-page "https://bioconductor.org/packages/ArrayExpress") + (synopsis "Building R objects from ArrayExpress datasets") + (description + "This package offers the possibility to access the ArrayExpress repository +at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data +structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") + (license license:artistic2.0))) + (define-public r-aseb (package (name "r-aseb") -- cgit v1.2.3 From c2cba91ac9b8f8d4ff860f9993280c35acc6cff7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 14:54:41 +0100 Subject: gnu: r-arrayexpress: Update to 1.57.0. * gnu/packages/bioconductor.scm (r-arrayexpress): Update to 1.57.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da7420d9f2..12a28dd6a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2475,13 +2475,13 @@ (define-public r-antiprofiles (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.56.0") + (version "1.57.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "0v2v7v0gim0bsg34ciplapz6mjih68yqhcgzdlhcyj2d6vrgiad5")))) + "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 01124e5a109bcae5ad59670eb855d479251acb9a Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 22 Jun 2022 15:45:33 +0200 Subject: gnu: Add r-asafe. * gnu/packages/bioconductor.scm (r-asafe): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12a28dd6a6..9c876704a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2497,6 +2497,29 @@ (define-public r-arrayexpress structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (license license:artistic2.0))) +(define-public r-asafe + (package + (name "r-asafe") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be +used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate +ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an +@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry +pairs.") + (license license:artistic2.0))) + (define-public r-aseb (package (name "r-aseb") -- cgit v1.2.3 From c706a0a2afd6ea2fa1905758970797cddeb150a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:02:41 +0100 Subject: gnu: r-asafe: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-asafe): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9c876704a0..4ac69d1a89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2500,13 +2500,13 @@ (define-public r-arrayexpress (define-public r-asafe (package (name "r-asafe") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From 6c7f0849c1e01bd9a3252643a7dd4442c4d9fc14 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 16 Jun 2022 18:35:02 +0200 Subject: gnu: Add r-alphabeta. * gnu/packages/bioconductor.scm (r-alphabeta): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ac69d1a89..92a3bc5a15 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2301,6 +2301,45 @@ (define-public r-aldex2 ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alphabeta + (package + (name "r-alphabeta") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlphaBeta" version)) + (sha256 + (base32 + "1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag")))) + (properties `((upstream-name . "AlphaBeta"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AlphaBeta") + (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants") + (description + "The package @code{AlphaBeta} is a computational method for estimating +epimutation rates and spectra from high-throughput DNA methylation data in +plants. The method has been specifically designed to: + +@itemize +@item analyze @emph{germline} epimutations in the context of + multi-generational mutation accumulation lines; +@item analyze @emph{somatic} epimutations in the context of plant development + and aging. +@end itemize") + (license license:gpl3))) + (define-public r-alpine (package (name "r-alpine") -- cgit v1.2.3 From 610616d4489fe9c066ffab4bc17f95f5cec40339 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:13:50 +0100 Subject: gnu: r-alphabeta: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92a3bc5a15..330ab8c77d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,13 +2304,13 @@ (define-public r-aldex2 (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag")))) + "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5dc82a7f8b08d0e7816107e60625badb090ad97a Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 16 Jun 2022 18:16:50 +0200 Subject: gnu: Add r-alevinqc. * gnu/packages/bioconductor.scm (r-alevinqc): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 330ab8c77d..975e36bb54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2301,6 +2301,40 @@ (define-public r-aldex2 ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alevinqc + (package + (name "r-alevinqc") + (version "1.12.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alevinQC" version)) + (sha256 + (base32 + "0g75qnz7ah0widdjn99lhvnacz38vgl9j86n65wyswsf413hz3bb")))) + (properties `((upstream-name . "alevinQC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-rcpp + r-rjson + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-tximport)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/csoneson/alevinQC") + (synopsis "Quality control reports for @code{Alevin} output") + (description + "The package @code{r-alevinqc} generates quality control reports +summarizing the output from an @code{alevin} run. The reports can be +generated as HTML or PDF files, or as Shiny applications.") + (license license:expat))) + (define-public r-alphabeta (package (name "r-alphabeta") -- cgit v1.2.3 From 6f39e161241931f101f3c7924bfa4ece34959604 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:28:15 +0100 Subject: gnu: r-alevinqc: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 975e36bb54..cd9fa0d2fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,13 +2304,13 @@ (define-public r-aldex2 (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "0g75qnz7ah0widdjn99lhvnacz38vgl9j86n65wyswsf413hz3bb")))) + "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2e85d26ebb5be6f7c52a9f2d780e0ae34fd40692 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 2 May 2022 11:49:55 +0200 Subject: gnu: Add r-aims. * gnu/packages/bioconductor.scm (r-aims): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd9fa0d2fe..179551c2f0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2107,6 +2107,30 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aims + (package + (name "r-aims") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AIMS" version)) + (sha256 + (base32 + "1z7yzaizyzcv556w8880603nd947k0d6raadjm42mdl66mma0cdx")))) + (properties `((upstream-name . "AIMS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071)) + (home-page "https://git.bioconductor.org/packages/AIMS") + (synopsis + "Absolute assignment of breast cancer intrinsic molecular subtype") + (description + "This package contains an implementation of @code{AIMS} -- Absolute +Intrinsic Molecular Subtyping. It contains necessary functions to assign the +five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, +Basal-like, Normal-like). Assignments could be done on individual samples as +well as on dataset of gene expression data.") + (license license:artistic2.0))) + (define-public r-airpart (package (name "r-airpart") -- cgit v1.2.3 From fa59a22140bcb98fa6e5cf895deaa5f2fbdb9bcf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:36:18 +0100 Subject: gnu: r-aims: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-aims): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 179551c2f0..61f312e17f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2110,13 +2110,13 @@ (define-public r-agimicrorna (define-public r-aims (package (name "r-aims") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "1z7yzaizyzcv556w8880603nd947k0d6raadjm42mdl66mma0cdx")))) + "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) -- cgit v1.2.3 From 8d3bd8e4b08fef0ea7fac48296191d3e6e342e9c Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 19 Jun 2022 22:42:01 +0200 Subject: gnu: Add r-ancombc. * gnu/packages/bioconductor.scm (r-ancombc): New variable. --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61f312e17f..d9303b5873 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2284,6 +2284,52 @@ (define-public r-anaquin analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) +(define-public r-ancombc + (package + (name "r-ancombc") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANCOMBC" version)) + (sha256 + (base32 + "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq")))) + (properties `((upstream-name . "ANCOMBC"))) + (build-system r-build-system) + (propagated-inputs + (list r-desctools + r-doparallel + r-dorng + r-dplyr + r-energy + r-foreach + r-hmisc + r-magrittr + r-mass + r-microbiome + r-nlme + r-nloptr + r-phyloseq + r-rdpack + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FrederickHuangLin/ANCOMBC") + (synopsis "Analysis of compositions of microbiomes with bias correction") + (description + "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA) +and correlation analyses for microbiome data. Specifically, the package +includes @dfn{Analysis of Compositions of Microbiomes with Bias +Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM) +for DA analysis, and @dfn{Sparse Estimation of Correlations among +Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically +subject to two sources of biases: unequal sampling fractions (sample-specific +biases) and differential sequencing efficiencies (taxon-specific biases). +Methodologies included in the @code{ANCOMBC} package were designed to correct +these biases and construct statistically consistent estimators.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") -- cgit v1.2.3 From 90d8ac279fcffe12969e0bdd43a07363c212942e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:28:28 +0100 Subject: gnu: Add r-treesummarizedexperiment. * gnu/packages/bioconductor.scm (r-treesummarizedexperiment): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9303b5873..17d5195ce5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8989,6 +8989,39 @@ (define-public r-treeio platform for merging tree with associated data and converting file formats.") (license license:artistic2.0))) +(define-public r-treesummarizedexperiment + (package + (name "r-treesummarizedexperiment") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "TreeSummarizedExperiment" version)) + (sha256 + (base32 + "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2")))) + (properties `((upstream-name . "TreeSummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-iranges + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-treeio)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment") + (synopsis "S4 class for data with tree structures") + (description + "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to +include hierarchical information on the rows or columns of the rectangular +data.") + (license license:gpl2+))) + (define-public r-ggtree (package (name "r-ggtree") -- cgit v1.2.3 From 139da51753717a06692bd87a754f54b4e60f4fcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:59:52 +0100 Subject: gnu: Add r-mia. * gnu/packages/bioconductor.scm (r-mia): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 17d5195ce5..0d4110bc20 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10027,6 +10027,54 @@ (define-public r-bumphunter studies.") (license license:artistic2.0))) +(define-public r-mia + (package + (name "r-mia") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "mia" version)) + (sha256 + (base32 + "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync")))) + (properties `((upstream-name . "mia"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-decipher + r-decontam + r-delayedarray + r-delayedmatrixstats + r-dirichletmultinomial + r-dplyr + r-iranges + r-mass + r-multiassayexperiment + r-rlang + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/microbiome/mia") + (synopsis "Microbiome analysis") + (description + "The mia package implements tools for microbiome analysis based on the +@code{SummarizedExperiment}, @code{SingleCellExperiment} and +@code{TreeSummarizedExperiment} infrastructure. Data wrangling and analysis +in the context of taxonomic data is the main scope. Additional functions for +common task are implemented such as community indices calculation and +summarization.") + (license license:artistic2.0))) + (define-public r-microbiome (package (name "r-microbiome") -- cgit v1.2.3 From c29d999a34d7dbb447446e0abd376ec3a27fdf54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 18:00:09 +0100 Subject: gnu: r-ancombc: Update to 2.0.1. * gnu/packages/bioconductor.scm (r-ancombc): Update to 2.0.1. [propagated-inputs]: Remove r-microbiome, r-nlme, and r-phyloseq; add r-cvxr, r-emmeans, r-lme4, r-lmertest, r-mia, r-rngtools, r-s4vectors, r-singlecellexperiment, r-summarizedexperiment, and r-treesummarizedexperiment. --- gnu/packages/bioconductor.scm | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d4110bc20..bb319a13e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2287,33 +2287,40 @@ (define-public r-anaquin (define-public r-ancombc (package (name "r-ancombc") - (version "1.6.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq")))) + "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs - (list r-desctools + (list r-cvxr + r-desctools r-doparallel r-dorng r-dplyr + r-emmeans r-energy r-foreach r-hmisc + r-lme4 + r-lmertest r-magrittr r-mass - r-microbiome - r-nlme + r-mia r-nloptr - r-phyloseq r-rdpack r-rlang + r-rngtools + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment r-tibble - r-tidyr)) + r-tidyr + r-treesummarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/FrederickHuangLin/ANCOMBC") (synopsis "Analysis of compositions of microbiomes with bias correction") -- cgit v1.2.3 From 059d38dc3f8b087f4a42df586daeb05761ee18d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 28 Nov 2022 11:20:23 +0100 Subject: gnu: Add r-glmgampoi. * gnu/packages/bioconductor.scm (r-glmgampoi): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb319a13e5..39c9c6f809 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8765,6 +8765,41 @@ (define-public r-glimma information.") (license license:lgpl3))) +(define-public r-glmgampoi + (package + (name "r-glmgampoi") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "glmGamPoi" version)) + (sha256 + (base32 + "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip")))) + (properties `((upstream-name . "glmGamPoi"))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-biocgenerics + r-delayedarray + r-delayedmatrixstats + r-hdf5array + r-matrixgenerics + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rlang + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/const-ae/glmGamPoi") + (synopsis "Fit a Gamma-Poisson Generalized Linear Model") + (description + "Fit linear models to overdispersed count data. The package can estimate +the overdispersion and fit repeated models for matrix input. It is designed +to handle large input datasets as they typically occur in single cell RNA-seq +experiments.") + (license license:gpl3))) + (define-public r-rots (package (name "r-rots") -- cgit v1.2.3 From 08fb5279a566d1ff4531fe9c741a97f0bce525b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 29 Nov 2022 15:21:54 +0100 Subject: gnu: r-nmf: Update to 0.25. * gnu/packages/bioconductor.scm (r-nmf): Update to 0.25. [propagated-inputs]: Remove r-pkgmaker; add r-codetools. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39c9c6f809..d38e2bc884 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4216,18 +4216,19 @@ (define-public r-jetset (define-public r-nmf (package (name "r-nmf") - (version "0.24.0") + (version "0.25") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628")))) + "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs (list r-cluster + r-codetools r-biobase r-biocmanager r-bigmemory ; suggested @@ -4238,7 +4239,6 @@ (define-public r-nmf r-foreach r-ggplot2 r-gridbase - r-pkgmaker r-rcolorbrewer r-registry r-reshape2 -- cgit v1.2.3 From 6b825d9cb96a56e5073615b7b0051e97a7ffb842 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Nov 2022 10:49:43 +0100 Subject: gnu: r-alpine: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-alpine): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d38e2bc884..744d3efb89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2454,13 +2454,13 @@ (define-public r-alphabeta (define-public r-alpine (package (name "r-alpine") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alpine" version)) (sha256 (base32 - "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + "0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0")))) (properties `((upstream-name . "alpine"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95e62fb9932e5e81d967ca61ba741c2f086bbc14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Nov 2022 10:49:47 +0100 Subject: gnu: r-biocparallel: Update to 1.32.3. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 744d3efb89..2ba2f3cb65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4787,13 +4787,13 @@ (define-public r-biomartr (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.1") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1fkfbs0n0sdssli7ibrswkfag080kgv8n1zf6ssxx729g1fz3m3h")))) + "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From cef2cbb295e1533e3ac6eff01240af61a4961b69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Nov 2022 10:49:48 +0100 Subject: gnu: r-biodb: Update to 1.6.1. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ba2f3cb65..62fb7cfcf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17855,14 +17855,14 @@ (define-public r-biocdockermanager (define-public r-biodb (package (name "r-biodb") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "08ahz3v2xbhwfh89dbnhhcdm0x5qv4hibi8wknlqf5x8gqm5j5w6")))) + "0mbqsias2ajw29d1wgl10y2cjqv3slrsgifccz0kh9l5r6bk28vz")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a712c07d6ada1160855c583556e854ccb48c47e1 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 29 Nov 2022 09:00:56 +0100 Subject: gnu: Add r-metaneighbor. * gnu/packages/bioconductor.scm (r-metaneighbor): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62fb7cfcf8..c62c5970b8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,6 +6010,42 @@ (define-public r-made4 datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-metaneighbor + (package + (name "r-metaneighbor") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MetaNeighbor" version)) + (sha256 + (base32 + "1gjjp5qlmv26sd3fvrd8cgv3invckxr8ldjpizpqm4mxjzifxwpm")))) + (properties `((upstream-name . "MetaNeighbor"))) + (build-system r-build-system) + (propagated-inputs + (list r-beanplot + r-dplyr + r-ggplot2 + r-gplots + r-igraph + r-matrix + r-matrixstats + r-rcolorbrewer + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MetaNeighbor") + (synopsis "Single cell replicability analysis") + (description + "This package implements a method to rapidly assess cell type identity using +both functional and random gene sets and it allows users to quantify cell type +replicability across datasets using neighbor voting. @code{MetaNeighbor} works +on the basis that cells of the same type should have more similar gene expression +profiles than cells of different types.") + (license license:expat))) + (define-public r-methylkit (package (name "r-methylkit") -- cgit v1.2.3 From 97b36ca4d3ab99190962a90da9627d559475dbd9 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 5 Dec 2022 16:21:51 +0100 Subject: gnu: Add r-makecdfenv. * gnu/packages/bioconductor.scm (r-makecdfenv): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62c5970b8..1d1aae322c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,6 +6010,33 @@ (define-public r-made4 datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an Affymetrix +@acronym{CDF, chip description file} and creates a hash table environment +containing the location/probe set membership mapping. The other one creates a +package that automatically loads that environment.") + (license license:gpl2+))) + (define-public r-metaneighbor (package (name "r-metaneighbor") -- cgit v1.2.3 From 85d5ce49015dfd93c1b3d37cafe83d017eedcfd4 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 5 Dec 2022 16:21:52 +0100 Subject: gnu: Add r-altcdfenvs. * gnu/packages/bioconductor.scm (r-altcdfenvs): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1d1aae322c..fbd23d0f6d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2492,6 +2492,37 @@ (define-public r-alpine data.") (license license:gpl2+))) +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with Affymetrix GeneChip short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read R connections in the FASTA format and it can +create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") -- cgit v1.2.3 From 8363719476f9bf5e4170435ad89d71f595d85853 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 5 Dec 2022 16:21:53 +0100 Subject: gnu: Add r-harshlight. * gnu/packages/bioconductor.scm (r-harshlight): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbd23d0f6d..07f8f658f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,6 +5854,33 @@ (define-public r-gseabase Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. Harshlight marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package +replaces the defected areas with @code{N/A}s or the median of the values of +the same probe. The new version handles the substitute value as a whole +matrix to solve the memory problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 5fb5af5658b7575a945579a7cf51c193600b76bb Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 5 Dec 2022 18:27:26 +0100 Subject: gnu: Add r-amplican. * gnu/packages/bioconductor.scm (r-amplican): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07f8f658f4..85c07605ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2202,6 +2202,53 @@ (define-public r-amountain in multi-layer WGCN using a continuous optimization approach.") (license license:gpl2+))) +(define-public r-amplican + (package + (name "r-amplican") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "amplican" version)) + (sha256 + (base32 + "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij")))) + (properties `((upstream-name . "amplican"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-biostrings + r-clustercrit + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggthemes + r-gridextra + r-gtable + r-iranges + r-knitr + r-matrix + r-matrixstats + r-rcpp + r-rmarkdown + r-s4vectors + r-shortread + r-stringr + r-waffle)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/valenlab/amplican") + (synopsis "Automated analysis of CRISPR experiments") + (description + "The package performs alignment of the amplicon reads, normalizes +gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) +and presents the results in the form of aggregated reports. Data and +statistics can be broken down by experiments, barcodes, user defined groups, +guides and amplicons allowing for quick identification of potential +problems.") + (license license:gpl3))) + (define-public r-amaretto (package (name "r-amaretto") -- cgit v1.2.3 From e0746ee4c4dab5b4bff9af4cb8b6256ef7888c42 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 7 Dec 2022 06:18:37 +0100 Subject: gnu: Add r-animalcules. * gnu/packages/bioconductor.scm (r-animalcules): New variable. --- gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85c07605ca..66fa69fade 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2384,6 +2384,65 @@ (define-public r-ancombc these biases and construct statistically consistent estimators.") (license license:artistic2.0))) +(define-public r-animalcules + (package + (name "r-animalcules") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "animalcules" version)) + (sha256 + (base32 + "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr")))) + (properties `((upstream-name . "animalcules"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-assertthat + r-biomformat + r-caret + r-covr + r-deseq2 + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-glmnet + r-gunifrac + r-lattice + r-limma + r-magrittr + r-matrix + r-multiassayexperiment + r-plotly + r-plotroc + r-rentrez + r-reshape2 + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-summarizedexperiment + r-tibble + r-tsne + r-umap + r-vegan + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/compbiomed/animalcules") + (synopsis "Interactive microbiome analysis toolkit") + (description + "Animalcules is an R package for utilizing up-to-date data analytics, +visualization methods, and machine learning models to provide users an +easy-to-use interactive microbiome analysis framework. It can be used as a +standalone software package or users can explore their data with the +accompanying interactive R Shiny application. Traditional microbiome analysis +such as alpha/beta diversity and differential abundance analysis are enhanced, +while new methods like biomarker identification are introduced by animalcules. +Powerful interactive and dynamic figures generated by animalcules enable users +to understand their data better and discover new insights.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") -- cgit v1.2.3 From 061ce5500abcaaf67c9e0cf09f8a881525a4fdef Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 8 Dec 2022 20:22:31 +0100 Subject: gnu: Add r-pepsnmr. * gnu/packages/bioconductor.scm (r-pepsnmr): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66fa69fade..1ceee9d77d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8514,6 +8514,35 @@ (define-public r-perfmeas a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) +(define-public r-pepsnmr + (package + (name "r-pepsnmr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "PepsNMR" version)) + (sha256 + (base32 + "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5")))) + (properties `((upstream-name . "PepsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-gridextra + r-matrix + r-matrixstats + r-ptw + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ManonMartin/PepsNMR") + (synopsis "Pre-process 1H-NMR FID signals") + (description + "This package provides R functions for common pre-processing steps that +are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data. It +also provides a function to read the @acronym{FID, free induction decay} +signals directly in the Bruker format.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package -- cgit v1.2.3 From b9014985beb92d040b7da195353b405c7c768378 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 8 Dec 2022 20:22:32 +0100 Subject: gnu: Add r-asics. * gnu/packages/bioconductor.scm (r-asics): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ceee9d77d..ec1bbb99d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2857,6 +2857,40 @@ (define-public r-asgsca model as latent variables.") (license license:gpl3))) +(define-public r-asics + (package + (name "r-asics") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASICS" version)) + (sha256 + (base32 + "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7")))) + (properties `((upstream-name . "ASICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-ggplot2 + r-glmnet + r-gridextra + r-matrix + r-mvtnorm + r-pepsnmr + r-plyr + r-quadprog + r-ropls + r-summarizedexperiment + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASICS") + (synopsis "Automatic statistical identification in complex spectra") + (description + "ASICS quantifies concentration of metabolites in a complex spectrum. +The identification of metabolites is performed by fitting a mixture model to +the spectra of the library with a sparse penalty.") + (license license:gpl2+))) + (define-public r-aspli (package (name "r-aspli") -- cgit v1.2.3 From 97ef08c20719b608560dc969549aed220a98f453 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 19 Dec 2022 16:03:41 +0100 Subject: gnu: Add r-cardelino. * gnu/packages/bioconductor.scm (r-cardelino): New variable. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec1bbb99d1..29768dc7c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3480,6 +3480,44 @@ (define-public r-biocgenerics packages.") (license license:artistic2.0))) +(define-public r-cardelino + (package + (name "r-cardelino") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "cardelino" version)) + (sha256 + (base32 + "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs")))) + (properties `((upstream-name . "cardelino"))) + (build-system r-build-system) + (propagated-inputs (list r-combinat + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggtree + r-matrix + r-matrixstats + r-pheatmap + r-s4vectors + r-snpstats + r-variantannotation + r-vcfr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/single-cell-genetics/cardelino") + (synopsis "Clone identification from single cell data") + (description + "This package provides methods to infer clonal tree configuration for a +population of cells using single-cell RNA-seq data (scRNA-seq), and possibly +other data modalities. Methods are also provided to assign cells to inferred +clones and explore differences in gene expression between clones. These +methods can flexibly integrate information from imperfect clonal trees +inferred based on bulk exome-seq data, and sparse variant alleles expressed in +scRNA-seq data. A flexible beta-binomial error model that accounts for +stochastic dropout events as well as systematic allelic imbalance is used.") + (license license:gpl3))) + (define-public r-coverageview (package (name "r-coverageview") -- cgit v1.2.3 From 64ed2e8380eff18628c03a75a5fcdbb383e6f38a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:44 +0100 Subject: gnu: r-ancombc: Update to 2.0.2. * gnu/packages/bioconductor.scm (r-ancombc): Update to 2.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29768dc7c2..11d5a3c0cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2334,13 +2334,13 @@ (define-public r-anaquin (define-public r-ancombc (package (name "r-ancombc") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) + "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d7fda903543a0299f8f0b12522dc42d57e820eb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: gnu: r-bambu: Update to 3.0.5. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11d5a3c0cb..41f8cd8cc4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3292,13 +3292,13 @@ (define-public r-badregionfinder (define-public r-bambu (package (name "r-bambu") - (version "3.0.2") + (version "3.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) + "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 72f9c4312be3dde0e94153c4c388176a4c61cb9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: gnu: r-bandits: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41f8cd8cc4..daa6eeab45 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3335,13 +3335,13 @@ (define-public r-bambu (define-public r-bandits (package (name "r-bandits") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) + "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d2666970d16cbbcc40f321ca827777831c381865 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: gnu: r-damefinder: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-damefinder): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index daa6eeab45..0f0a5bc57b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3600,13 +3600,13 @@ (define-public r-dama (define-public r-damefinder (package (name "r-damefinder") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) + "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e757936b96ce519a0ad08c8c57945343b4692ec7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: gnu: r-deconvr: Update to 1.4.3. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.3. [propagated-inputs]: Add r-minfi. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f0a5bc57b..21986a70c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3914,13 +3914,13 @@ (define-public r-decontam (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) + "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -3936,6 +3936,7 @@ (define-public r-deconvr r-mass r-matrixstats r-methylkit + r-minfi r-nnls r-quadprog r-rsq -- cgit v1.2.3 From 74be5ec3e85ed02aaa4eeb22413c201961ad95c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: gnu: r-biocparallel: Update to 1.32.4. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21986a70c0..51ccb1a6f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4997,13 +4997,13 @@ (define-public r-biomartr (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5")))) + "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From db6ae57157506b1396641c9f6360483ec226d54c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: gnu: r-deseq2: Update to 1.38.2. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.2. [propagated-inputs]: Remove r-genefilter; add r-matrixstats. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51ccb1a6f1..f1e875633f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5364,26 +5364,26 @@ (define-public r-deseq (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) + "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-genefilter r-geneplotter r-genomicranges r-ggplot2 r-iranges r-locfit + r-matrixstats r-rcpp r-rcpparmadillo r-s4vectors -- cgit v1.2.3 From 6af97fcc0eef7e8577b3d5ceafe7be2c7592bb6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: gnu: r-edger: Update to 3.40.1. * gnu/packages/bioconductor.scm (r-edger): Update to 3.40.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1e875633f..9557cb736a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5596,13 +5596,13 @@ (define-public r-edaseq (define-public r-edger (package (name "r-edger") - (version "3.40.0") + (version "3.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) + "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a71a89ac39f81ab8b6902f25ff12e9d1bb4fb7d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: gnu: r-genefilter: Update to 1.80.2. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9557cb736a..790eef98d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5721,14 +5721,14 @@ (define-public r-gage (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.0") + (version "1.80.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) + "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) -- cgit v1.2.3 From 86fcb20aa839c069c553b3dcb5c2ca4f9be3ee24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: gnu: r-genomeinfodb: Update to 1.34.4. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 790eef98d7..86b9dc0123 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5811,13 +5811,13 @@ (define-public r-genomation (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.3") + (version "1.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) + "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From a4362f4599fd8f7a0912b74830608d5c7f2d2604 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: gnu: r-genomicfeatures: Update to 1.50.3. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86b9dc0123..1f648012bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5871,13 +5871,13 @@ (define-public r-genomicalignments (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.2") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) + "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From b035f07cc2eaf5c5955a949862844fc74fbb6269 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: gnu: r-genomicranges: Update to 1.50.2. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.50.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f648012bb..97d36bac9d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5949,13 +5949,13 @@ (define-public r-genomicfiles (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.50.1") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) + "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 53fb765c85601cd35b8d73f28d77536b3127ad62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: gnu: r-impute: Update to 1.72.2. * gnu/packages/bioconductor.scm (r-impute): Update to 1.72.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97d36bac9d..91d62d4b30 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6112,13 +6112,13 @@ (define-public r-rhtslib (define-public r-impute (package (name "r-impute") - (version "1.72.1") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) + "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) (native-inputs (list gfortran)) (build-system r-build-system) -- cgit v1.2.3 From 5fc338637b08a4791b3bc84897c1d227c80011c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: gnu: r-lfa: Update to 1.28.1. * gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d62d4b30..a6e39f986a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6181,13 +6181,13 @@ (define-public r-keggrest (define-public r-lfa (package (name "r-lfa") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) + (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) -- cgit v1.2.3 From dc6f9ab3ab3f64a26af7c99f86b5f7bc20f48957 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: gnu: r-scmap: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6e39f986a..24e166fd18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7314,13 +7314,13 @@ (define-public r-scdblfinder (define-public r-scmap (package (name "r-scmap") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) + (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9e18e3a372d738f9cc7722613db1e876dbfe9e4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: gnu: r-tximport: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24e166fd18..90df6bac1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7861,13 +7861,13 @@ (define-public r-topgo (define-public r-tximport (package (name "r-tximport") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) + "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From a13f5a52d05ec94ed0d788ec586ad979276fa34e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: gnu: r-oligo: Update to 1.62.1. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90df6bac1e..8a38836afe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8234,14 +8234,14 @@ (define-public r-oligoclasses (define-public r-oligo (package (name "r-oligo") - (version "1.62.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) + "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From c47fd0c47c3dbe523af9bdf109d3ea47d24dd53c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: gnu: r-diffbind: Update to 3.8.3. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a38836afe..81241f85de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8379,14 +8379,14 @@ (define-public r-greylistchip (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.1") + (version "3.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) + "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 96508fa43aa5f122a84c5b8ed1f41fabceada197 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: gnu: r-glmgampoi: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81241f85de..19379d95b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9097,13 +9097,13 @@ (define-public r-glimma (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip")))) + "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b51001141bd36d939bcd60ac9f6b1bc459562545 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: gnu: r-dnacopy: Update to 1.72.2. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19379d95b9..397fb788a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9624,14 +9624,14 @@ (define-public r-copynumber (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) + "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) -- cgit v1.2.3 From 2eb81c0888a3784658e7d7cfe4426994863280a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: gnu: r-lpsymphony: Update to 1.26.2. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 397fb788a0..8afed238c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9782,14 +9782,14 @@ (define-public r-karyoploter (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) + "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) (build-system r-build-system) (arguments (list -- cgit v1.2.3 From ceffbc313fa945be32fe5702227b93a497657f9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: gnu: r-linnorm: Update to 2.22.1. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8afed238c5..2da844b822 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10671,14 +10671,14 @@ (define-public r-lumi (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.0") + (version "2.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) + "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 72053845339db0237107c18ee3d85aa68aadf49c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: gnu: r-sigpathway: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2da844b822..ac9d49db73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11019,14 +11019,14 @@ (define-public r-anota (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) + "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") -- cgit v1.2.3 From 2e10df101f76154b6d5a64f9c295c2402b01ad18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: gnu: r-enrichplot: Update to 1.18.3. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac9d49db73..b1c5b7db3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11141,14 +11141,14 @@ (define-public r-dose (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.18.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) + "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl")))) (build-system r-build-system) (propagated-inputs (list r-aplot -- cgit v1.2.3 From da24c1c9495ba414d786cf69c6c73009ce2a4756 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: gnu: r-clusterexperiment: Update to 2.18.1. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1c5b7db3c..457e988b80 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11219,13 +11219,13 @@ (define-public r-clusterprofiler (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) + "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) -- cgit v1.2.3 From 7f45db2df8b6ad47a4da0ef9f6a25bb4d887213d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: gnu: r-aucell: Update to 1.20.2. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.20.2. [propagated-inputs]: Add r-matrix. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 457e988b80..050650de87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11988,14 +11988,14 @@ (define-public r-allelicimbalance (define-public r-aucell (package (name "r-aucell") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) + "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -12004,6 +12004,7 @@ (define-public r-aucell r-delayedarray r-delayedmatrixstats r-gseabase + r-matrix r-mixtools r-r-utils r-shiny -- cgit v1.2.3 From 90b10b37e8ef9cd9b1409be74bd0d45d9b3cc1ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: gnu: r-iclusterplus: Update to 1.34.2. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 050650de87..5b684a4e64 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12825,14 +12825,14 @@ (define-public r-biocfilecache (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) + "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) -- cgit v1.2.3 From 5ac36a82e86a179c4b851cac1045fa2bdac3dc02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: gnu: r-rsubread: Update to 2.12.2. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5b684a4e64..db3faf7efe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13265,14 +13265,14 @@ (define-public r-annotatr (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.0") + (version "2.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) + "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) -- cgit v1.2.3 From 7edcbf84bf2fae8e1d58d086f645fb7c21fb65aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: gnu: r-ggcyto: Update to 1.26.4. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.26.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db3faf7efe..761a878cdb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13498,14 +13498,14 @@ (define-public r-ncdfflow (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) + "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 031dbcbd0e32208574b770700a35fef2138a5719 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: gnu: r-opencyto: Update to 2.10.1. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.10.1. [propagated-inputs]: Remove r-clue, r-flowstats, r-gtools, r-ks, r-lattice, r-mass, r-plyr, r-r-utils, r-rcpp, and r-rrcov; add r-bh and r-cpp11. --- gnu/packages/bioconductor.scm | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 761a878cdb..90ae32877a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13721,38 +13721,30 @@ (define-public r-flowstats (define-public r-opencyto (package (name "r-opencyto") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) + "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-bh + r-biobase r-biocgenerics - r-clue + r-cpp11 r-data-table r-flowclust r-flowcore - r-flowstats r-flowviz r-flowworkspace r-graph - r-gtools - r-ks - r-lattice - r-mass r-ncdfflow - r-plyr - r-r-utils r-rbgl - r-rcolorbrewer - r-rcpp - r-rrcov)) + r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") -- cgit v1.2.3 From fc617e70e655470101b6c599cc0be11b5b672e00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: gnu: r-rcistarget: Update to 1.18.2. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.18.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90ae32877a..679b6dc183 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13944,14 +13944,14 @@ (define-public r-depecher (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.17.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) + "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 18468f775e49a32df89a39f9a808d5c1880d8364 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: gnu: r-biocviews: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.1. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 679b6dc183..730e3b417f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15614,13 +15614,13 @@ (define-public r-biocstyle (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) + "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -15632,6 +15632,7 @@ (define-public r-biocviews r-rcurl r-xml r-runit)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that -- cgit v1.2.3 From e895da0406bb5053cdc85b374938b091f7db79df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: gnu: r-preprocesscore: Update to 1.60.1. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 730e3b417f..764af84960 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16201,14 +16201,14 @@ (define-public r-fourcseq (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) + "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit v1.2.3 From 68701917b8c8458cff6e41e78ebcea5d45b9875e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: gnu: r-s4vectors: Update to 0.36.1. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 764af84960..7af0634daa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16222,13 +16222,13 @@ (define-public r-preprocesscore (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) + "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From c4cbfa40d8d9b3619b987a360322ee105c78f76e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: gnu: r-chromvar: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7af0634daa..34e11fc28f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16712,13 +16712,13 @@ (define-public r-motifmatchr (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) + (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 71c115fd943fc20de6112904a523c3c72993c08d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: gnu: r-scuttle: Update to 1.8.3. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34e11fc28f..b55f11a741 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16819,14 +16819,14 @@ (define-public r-singler (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) + "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cfa8d448bcc1c4aa83b61797ed45e4560894356f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: gnu: r-scran: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-scran): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b55f11a741..c1e6c4c002 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16899,14 +16899,14 @@ (define-public r-scater (define-public r-scran (package (name "r-scran") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) + "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) (build-system r-build-system) (propagated-inputs (list r-beachmat -- cgit v1.2.3 From fd4ca4a2661cba23e7ee688628a1a4a0ee1d943f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: gnu: r-kegggraph: Update to 1.58.3. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.58.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1e6c4c002..53c7d048c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17501,13 +17501,13 @@ (define-public r-gwascat (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.58.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) + (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3072990b03561ceb8517f7860a2b357e56f95395 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:07:58 +0100 Subject: gnu: r-biocparallel: Update to 1.32.5. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.5. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53c7d048c9..eacddb8caf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus +;;; Copyright © 2015-2023 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -4997,13 +4997,13 @@ (define-public r-biomartr (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.4") + (version "1.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym")))) + "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From b37a9bfba6ea535d05589ea7f96f3918e0140f21 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:35 +0100 Subject: gnu: r-bsgenome: Update to 1.66.2. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.66.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eacddb8caf..59ac8d9e97 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5118,13 +5118,13 @@ (define-public r-biovizbase (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.66.1") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm")))) + "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From f5629558b174dfa4f72004ab8933cb206873923c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:35 +0100 Subject: gnu: r-genomeinfodb: Update to 1.34.6. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.6. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59ac8d9e97..2ba7c672bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5811,13 +5811,13 @@ (define-public r-genomation (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.4") + (version "1.34.6") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r")))) + "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From aca59da9317cf9ff8d1a71254008d9d0bb5a86b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:35 +0100 Subject: gnu: r-msnbase: Update to 2.24.2. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.24.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ba7c672bc..3ed0f24818 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6483,14 +6483,14 @@ (define-public r-mutationalpatterns (define-public r-msnbase (package (name "r-msnbase") - (version "2.24.0") + (version "2.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "16apm4qn7sbv06pk2i8k5z7qgkv0yq0h8ri32vikdplqxxh7h0cz")))) + "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3ac0f4e62c7708907c0ea810b5f983ff1fe6c658 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:35 +0100 Subject: gnu: r-batchelor: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3ed0f24818..4fa3d304d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9916,14 +9916,14 @@ (define-public r-residualmatrix (define-public r-batchelor (package (name "r-batchelor") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1cdpq8zfn718qmsqjp79siddh3kzag4a90p276v261xbjvrxavjv")))) + "1yj84ba6px14hbqg8526527vfcxmzvmly34f7hba4vybdm1jscfm")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 850638df5abb5db923d02b0c6ab1fc5b8a1aad97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:36 +0100 Subject: gnu: r-flowworkspace: Update to 4.10.1. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.10.1. [propagated-inputs]: Remove r-aws-s3, r-aws-signature, r-digest, r-lattice, r-latticeextra, r-rcpp, r-rcpparmadillo, and r-rcppparallel; add r-cpp11. --- gnu/packages/bioconductor.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4fa3d304d5..0501ec270f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13629,38 +13629,31 @@ (define-public r-rprotobuflib (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.10.0") + (version "4.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "07w2pnnzmivfc621c8pvndqrn1k245cwjrb0nnk2i85i3si4j9c3")))) + "0jmbfclkfm0n2mshk94906kivii7awlskf7l7ydn8ki8wrpzxqg4")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - (list r-aws-s3 - r-aws-signature - r-bh + (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-data-table r-delayedarray - r-digest r-dplyr r-flowcore r-ggplot2 r-graph - r-lattice - r-latticeextra r-matrixstats r-ncdfflow r-rbgl - r-rcpp - r-rcpparmadillo - r-rcppparallel r-rgraphviz r-rhdf5lib r-rprotobuflib -- cgit v1.2.3 From d41e85678a7b92fbd92faa7b48df87914d40710f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:36 +0100 Subject: gnu: r-variancepartition: Update to 1.28.1. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.1. [propagated-inputs]: Add r-remacor. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0501ec270f..4109dceb6b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14639,14 +14639,14 @@ (define-public r-wavetiling (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1mn91r0yrhz08m3vs2h3i35rcbxyc7sdfknmk6vcw1z75znjsnpl")))) + "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -14667,6 +14667,7 @@ (define-public r-variancepartition r-pbkrtest r-progress r-rdpack + r-remacor r-reshape2 r-rhpcblasctl r-rlang -- cgit v1.2.3 From 8ee7f8df76c882cc464c9cf164bcaedce616ed05 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:36 +0100 Subject: gnu: r-biocviews: Update to 1.66.2. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4109dceb6b..3d7c47d0e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15608,13 +15608,13 @@ (define-public r-biocstyle (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.1") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02")))) + "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 8423ca9da8f7db8221548500ce3042532adb2e4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 9 Jan 2023 23:08:36 +0100 Subject: gnu: r-biocset: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d7c47d0e5..c2fa26cb59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15854,14 +15854,14 @@ (define-public r-biocpkgtools (define-public r-biocset (package (name "r-biocset") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8")))) + "1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3e1c85b7ec9e694168dd322dcc93866b666beba9 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Fri, 13 Jan 2023 16:07:16 +0100 Subject: gnu: Add r-maser. * gnu/packages/bioconductor.scm (r-maser): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2fa26cb59..ca236bcf75 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6274,6 +6274,38 @@ (define-public r-makecdfenv package that automatically loads that environment.") (license license:gpl2+))) +(define-public r-maser + (package + (name "r-maser") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "maser" version)) + (sha256 + (base32 + "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv")))) + (properties `((upstream-name . "maser"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-dplyr + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-reshape2 + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/DiogoVeiga/maser") + (synopsis "Mapping alternative splicing events to proteins") + (description + "This package provides functionalities for downstream analysis, annotation +and visualizaton of alternative splicing events generated by rMATS.") + (license license:expat))) + (define-public r-metaneighbor (package (name "r-metaneighbor") -- cgit v1.2.3 From 4f7ef3f5284054c5d56b2ce7609ebf57a51e00eb Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 18 Jan 2023 18:35:58 +0100 Subject: gnu: Add r-breakpointrdata. * gnu/packages/bioconductor.scm (r-breakpointrdata): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca236bcf75..84a701d038 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1291,6 +1291,26 @@ (define-public r-biscuiteerdata biscuiteer.") (license license:gpl3))) +(define-public r-breakpointrdata + (package + (name "r-breakpointrdata") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointRdata" version 'experiment)) + (sha256 + (base32 + "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn")))) + (properties `((upstream-name . "breakpointRdata"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/breakpointRdata") + (synopsis "Strand-seq data for demonstration purposes") + (description + "This package is a collection of Strand-seq data. The main purpose is to +demonstrate functionalities of the @code{breakpointR} package.") + (license license:expat))) + (define-public r-celldex (package (name "r-celldex") -- cgit v1.2.3 From fda2d75d8d886ac32e20b7c5cebff378f2e374b9 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 18 Jan 2023 18:35:59 +0100 Subject: gnu: Add r-breakpointr. * gnu/packages/bioconductor.scm (r-breakpointr): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84a701d038..93c6165b62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3500,6 +3500,40 @@ (define-public r-biocgenerics packages.") (license license:artistic2.0))) +(define-public r-breakpointr + (package + (name "r-breakpointr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointR" version)) + (sha256 + (base32 + "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx")))) + (properties `((upstream-name . "breakpointR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-breakpointrdata + r-cowplot + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/BreakPointR") + (synopsis "Find breakpoints in Strand-seq data") + (description + "This package implements functions for finding breakpoints, plotting and +export of Strand-seq data.") + (license license:expat))) + (define-public r-cardelino (package (name "r-cardelino") -- cgit v1.2.3 From f145afd16f1a20c56ebd937b407cb4ad8c32f0e5 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Tue, 17 Jan 2023 18:30:39 +0100 Subject: gnu: Add r-scistreer. * gnu/packages/bioconductor.scm (r-scistreer): New variable. --- gnu/packages/bioconductor.scm | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93c6165b62..6d16a99c36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2022 Efraim Flashner ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice -;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier +;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka @@ -7397,6 +7397,43 @@ (define-public r-scdblfinder comprehensive scDblFinder method.") (license license:gpl3))) +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scistreer + (package + (name "r-scistreer") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "scistreer" version)) + (sha256 + (base32 + "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) + (properties `((upstream-name . "scistreer"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-dplyr + r-ggplot2 + r-ggtree + r-igraph + r-paralleldist + r-patchwork + r-phangorn + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-reshape2 + r-rhpcblasctl + r-stringr + r-tidygraph)) + (home-page "https://github.com/kharchenkolab/scistreer") + (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") + (description + "This package provides fast maximum-likelihood phylogeny inference from +noisy single-cell data using the ScisTree algorithm proposed by +@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the +method applicable to massive single-cell datasets (>10,000 cells).") + (license license:gpl3))) + (define-public r-scmap (package (name "r-scmap") -- cgit v1.2.3 From c31d8adcb0e4d5780583f26d51a1b4d3552783f2 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Tue, 17 Jan 2023 18:30:41 +0100 Subject: gnu: Add r-numbat. * gnu/packages/bioconductor.scm (r-numbat): New variable. --- gnu/packages/bioconductor.scm | 67 +++++++++++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 2 +- 2 files changed, 68 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d16a99c36..f1760b2007 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6750,6 +6750,73 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. It does not require +tumor/normal-paired DNA or genotype data, but operates solely on the donor +scRNA-data data (for example, 10x Cell Ranger output). It can be used to: + +@enumerate +@item detect allele-specific copy number variations from single-cells +@item differentiate tumor versus normal cells in the tumor microenvironment +@item infer the clonal architecture and evolutionary history of profiled tumors +@end enumerate + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aad49b4524..38e1a84282 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9232,7 +9232,7 @@ (define-public r-roptim (description "This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms -('Nelder-Mead', BFGS', CG', L-BFGS-B and SANN') underlying @code{optim()}.") +(Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.") (license license:gpl2+))) (define-public r-base64url -- cgit v1.2.3 From 072f605c125f98bf69cf25ec5a6caf791c72920b Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Fri, 20 Jan 2023 09:58:00 +0100 Subject: gnu: Add r-scds. * gnu/packages/bioconductor.scm (r-scds): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1760b2007..6f2c7380fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet +;;; Copyright © 2023 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; @@ -7782,6 +7783,34 @@ (define-public r-trajectoryutils structures to hold pseudotime inference results.") (license license:gpl3))) +(define-public r-scds + (package + (name "r-scds") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scds" version)) + (sha256 + (base32 + "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + (properties `((upstream-name . "scds"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-matrix + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scds") + (synopsis "In-silico doublet annotation for single cell RNA sequencing data") + (description + "This is an R package for doublet annotation of single cell RNA +sequencing data. @code{scds} provides methods to annotate doublets in +scRNA-seq data computationally.") + (license license:expat))) + (define-public r-slingshot (package (name "r-slingshot") -- cgit v1.2.3 From b374a45eb0468189140c19b5cebcf8282eb6c20a Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 17 Jan 2023 13:25:37 +0100 Subject: gnu: Add r-speaq. * gnu/packages/bioconductor.scm (r-speaq): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f2c7380fb..343a500fc3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Peter Lo -;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu +;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes @@ -7843,6 +7843,46 @@ (define-public r-slingshot graph construction.") (license license:artistic2.0))) +;; This is a CRAN package but it depends on a bionconductor package. +(define-public r-speaq + (package + (name "r-speaq") + (version "2.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "speaq" version)) + (sha256 + (base32 + "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) + (properties `((upstream-name . "speaq"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-data-table + r-dosnow + r-foreach + r-ggplot2 + r-gridextra + r-impute + r-massspecwavelet + r-missforest + r-reshape2 + r-rfast + r-rvest + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=speaq") + (synopsis "Tools for nuclear magnetic resonance spectra alignment") + (description + "This package helps with @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy +data analysis as easy as possible. It only requires a small set of functions to +perform an entire analysis. Speaq offers the possibility of raw spectra alignment +and quantitation but also an analysis based on features whereby the spectra are +converted to peaks which are then grouped and turned into features. These features +can be processed with any number of statistical tools either included in speaq +or available elsewhere on CRAN.") + (license license:asl2.0))) + (define-public r-stager (package (name "r-stager") -- cgit v1.2.3 From 3d9516344e190e670257bf49a937a4c33f1d989a Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 17 Jan 2023 13:25:38 +0100 Subject: gnu: Add r-alpsnmr. * gnu/packages/bioconductor.scm (r-alpsnmr): New variable. --- gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 343a500fc3..7b6515a639 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2619,6 +2619,59 @@ (define-public r-alpine data.") (license license:gpl2+))) +(define-public r-alpsnmr + (package + (name "r-alpsnmr") + (version "4.0.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlpsNMR" version)) + (sha256 + (base32 + "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + (properties `((upstream-name . "AlpsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-baseline + r-biocparallel + r-dplyr + r-fs + r-future + r-generics + r-ggplot2 + r-glue + r-htmltools + r-magrittr + r-matrixstats + r-mixomics + r-pcapp + r-purrr + r-readxl + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-signal + r-speaq + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://sipss.github.io/AlpsNMR/") + (synopsis "Automated spectral processing system for NMR") + (description + "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data +directories both zipped and unzipped. It provides automated and efficient +signal processing for untargeted NMR metabolomics. It is able to interpolate +the samples, detect outliers, exclude regions, normalize, detect peaks, align +the spectra, integrate peaks, manage metadata and visualize the spectra. +After spectra processing, it can apply multivariate analysis on extracted +data. Efficient plotting with 1-D data is also available. Basic reading of +1D ACD/Labs exported JDX samples is also available.") + (license license:expat))) + (define-public r-altcdfenvs (package (name "r-altcdfenvs") -- cgit v1.2.3 From 9fc3e4fb266903eb8b3eb9434c3cc84c64da5aed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 22 Jan 2023 09:12:50 +0100 Subject: gnu: r-speaq: Fix description. * gnu/packages/bioconductor.scm (r-speaq)[description]: Reword. --- gnu/packages/bioconductor.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b6515a639..420940ff21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7896,7 +7896,7 @@ (define-public r-slingshot graph construction.") (license license:artistic2.0))) -;; This is a CRAN package but it depends on a bionconductor package. +;; This is a CRAN package but it depends on a bioconductor package. (define-public r-speaq (package (name "r-speaq") @@ -7927,13 +7927,13 @@ (define-public r-speaq (home-page "https://cran.r-project.org/package=speaq") (synopsis "Tools for nuclear magnetic resonance spectra alignment") (description - "This package helps with @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy -data analysis as easy as possible. It only requires a small set of functions to -perform an entire analysis. Speaq offers the possibility of raw spectra alignment -and quantitation but also an analysis based on features whereby the spectra are -converted to peaks which are then grouped and turned into features. These features -can be processed with any number of statistical tools either included in speaq -or available elsewhere on CRAN.") + "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance} +spectroscopy data analysis as easy as possible. It only requires a small set +of functions to perform an entire analysis. Speaq offers the possibility of +raw spectra alignment and quantitation but also an analysis based on features +whereby the spectra are converted to peaks which are then grouped and turned +into features. These features can be processed with any number of statistical +tools either included in speaq or available elsewhere on CRAN.") (license license:asl2.0))) (define-public r-stager -- cgit v1.2.3 From ac32f93df36f1908c3d90c28704e3b2bf9c91c36 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 17 Jan 2023 14:18:23 +0100 Subject: gnu: Add r-anvil. * gnu/packages/bioconductor.scm (r-anvil): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 420940ff21..711b988e7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2464,6 +2464,47 @@ (define-public r-animalcules to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-anvil + (package + (name "r-anvil") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnVIL" version)) + (sha256 + (base32 + "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv")))) + (properties `((upstream-name . "AnVIL"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocmanager + r-dplyr + r-dt + r-futile-logger + r-htmltools + r-httr + r-jsonlite + r-miniui + r-rapiclient + r-rlang + r-shiny + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnVIL") + (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") + (description + "The AnVIL is a cloud computing resource developed in part by the +National Human Genome Research Institute. The AnVIL package provides end-user +and developer functionality. AnVIL provides fast binary package installation, +utilities for working with Terra/AnVIL table and data resources, and +convenient functions for file movement to and from Google cloud storage. For +developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, +Dockstore, and Gen3 RESTful programming interface, including helper functions +to transform JSON responses to formats more amenable to manipulation in R.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") -- cgit v1.2.3