diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 375 |
1 files changed, 300 insertions, 75 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bfca85bbc..e54c9ccf2b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1482,6 +1482,47 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-hdcytodata + (package + (name "r-hdcytodata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDCytoData" version 'experiment)) + (sha256 + (base32 + "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc")))) + (properties `((upstream-name . "HDCytoData"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'avoid-internet-access + (lambda _ + (setenv "GUIX_BUILD" "yes") + (substitute* "R/zzz.R" + (("createHubAccessors.*" m) + (string-append + "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) + (propagated-inputs + (list r-experimenthub r-flowcore r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/lmweber/HDCytoData") + (synopsis + "Set of high-dimensional flow cytometry and mass cytometry benchmark datasets") + (description + "HDCytoData contains a set of high-dimensional cytometry benchmark +datasets. These datasets are formatted into SummarizedExperiment and flowSet +Bioconductor object formats, including all required metadata. Row metadata +includes sample IDs, group IDs, patient IDs, reference cell population or +cluster labels and labels identifying spiked in cells. Column metadata +includes channel names, protein marker names, and protein marker classes.") + (license license:expat))) + (define-public r-italicsdata (package (name "r-italicsdata") @@ -2775,18 +2816,19 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.0.2") + (version "4.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + "19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs (list r-baseline r-biocparallel + r-cli r-dplyr r-fs r-future @@ -3225,13 +3267,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) + "0j6jq1cll8440i2srmy4lbvvyqawailk9byl9bnnzln1mdgys8r7")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -3243,6 +3285,7 @@ variant.") r-genomicranges r-iranges r-matrix + r-matrixstats r-rsamtools r-s4vectors r-scales @@ -3519,13 +3562,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.5") + (version "3.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) + "072rys45f9nl4b2dq559qakjcp2990ncdw49j49761izxgc7byzs")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -3562,13 +3605,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) + "11w0azh2g0y331imqpllnb0csjxf3gs1767cc67c1zp0ykg6yq8l")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4441,14 +4484,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) + "04m51jdahhmj31cs2af9il5zijkpb255f9p06i8ga0v3g79gj1bp")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -5000,13 +5043,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.60.0") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) + "1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6181,13 +6224,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) + "1c784ic85v64gflwwk22dh3f0m60q3z6y23d9jy3w8ydhda6gw0s")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -6548,13 +6591,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.1") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) + (base32 "0z8aa2435f7v2l6zwv47v2a6p9hal156dsh8v1iri233d1qx7fax")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -6569,13 +6612,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.54.1") + (version "3.54.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0x6wkbw8v0hq9dfr433165jmii05rswjsm97dpxvyvxvya3sxqa1")))) + "1qch34znld9i8sy1xwpy23z2zs07nj39wkfmgfi7qw141vn6gr8b")))) (build-system r-build-system) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6880,6 +6923,75 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) +(define-public r-mmuphin + (package + (name "r-mmuphin") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MMUPHin" version)) + (sha256 + (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")) + ;; Delete generated files. + (snippet + '(for-each delete-file + '("inst/doc/MMUPHin.R" + "inst/doc/MMUPHin.html"))))) + (properties `((upstream-name . "MMUPHin"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-includes + (lambda _ + (substitute* "inst/doc/MMUPHin.Rmd" + (("\\.\\./man/figures") + (string-append (getcwd) "/man/figures")) + (("bibliography: references.bib") + (string-append "bibliography: " + (getcwd) "/vignettes/references.bib"))))) + ;; Maaslin2 generates log files with timestamps. We don't need to + ;; keep them. The generated PDF files also contain timestamps, so + ;; we replace them with arbitrary fixed timestamps. + (add-after 'check 'make-reproducible + (lambda _ + (for-each delete-file + (find-files #$output "maaslin2.log")) + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* (find-files #$output "\\.pdf$") + (("/CreationDate \\(D:.*\\)") + "/CreationDate (D:20230301143558)") + (("/ModDate \\(D:.*\\)") + "/ModDate (D:20230301143558)")))))))) + ;; The DESCRIPTION file says that glpk is needed, but this package does + ;; not seem to reference the library directly. + (propagated-inputs + (list r-cowplot + r-biocstyle + r-dplyr + r-fpc + r-ggplot2 + r-igraph + r-maaslin2 + r-metafor + r-stringr + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MMUPHin") + (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") + (description + "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. +It has function interfaces for: +@itemize +@item covariate-controlled batch- and cohort effect adjustment; +@item meta-analysis differential abundance testing; +@item meta-analysis unsupervised discrete structure (clustering) discovery; +@item meta-analysis unsupervised continuous structure discovery. +@end itemize") + (license license:expat))) + (define-public r-motifrg (package (name "r-motifrg") @@ -6910,14 +7022,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) + "061dgs3ygvr4vrc6mrmikqn4a7a5qajn7k8crbskdkg4svg8qv1a")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -6960,14 +7072,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.8.0") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) + "0d0fsc4x8psfd93asi2d5kq1888s963d3s8kcihd5knqah000mh8")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7222,13 +7334,13 @@ previously been used in XCMS.") (define-public r-numbat (package (name "r-numbat") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 - "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + "06qq7i8k1mi7yg1irfbk3d2fmk7awvzj7h7r54hnr6pzywk7nmhc")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -7356,6 +7468,32 @@ annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.") (license license:artistic2.0))) +(define-public r-oscope + (package + (name "r-oscope") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Oscope" version)) + (sha256 + (base32 + "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://bioconductor.org/packages/Oscope") + (synopsis + "Oscillatory genes identifier in unsynchronized single cell RNA-seq") + (description + "Oscope is a oscillatory genes identifier in unsynchronized single cell +RNA-seq. This statistical pipeline has been developed to identify and recover +the base cycle profiles of oscillating genes in an unsynchronized single cell +RNA-seq experiment. The Oscope pipeline includes three modules: a sine model +module to search for candidate oscillator pairs; a K-medoids clustering module +to cluster candidate oscillators into groups; and an extended nearest +insertion module to recover the base cycle order for each oscillator group.") + (license license:asl2.0))) + (define-public r-pcaexplorer (package (name "r-pcaexplorer") @@ -7972,13 +8110,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) + (base32 "00zqvjfn1pqza5gl3jfr10fvcrq6gpw9hfjcxjsm4f5p7ldnhpw0")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -8612,14 +8750,14 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.6.6") + (version "0.6.7") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph")))) + "1s8bjbban2a3cqhwgykmhkv5b748nscamfbv67v4cppjbdvlhb5s")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -9132,14 +9270,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.3") + (version "3.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) + "1gil19qk4wc695sl7r789xnqyv748n4jdhaighkjy5hfp9xaaax7")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -9850,13 +9988,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) + "1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -10712,16 +10850,28 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) + "1c0lc4abnb859x481ky6d3kc9zzxwvf4kqgwxyqapc4g72b4vh65")) + (snippet + '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (invoke "esbuild" + (assoc-ref inputs "js-jquery-sticky-kit") + "--minify" + "--outfile=docs/jquery.sticky-kit.min.js")))))) (propagated-inputs (list r-abind r-biobase @@ -10736,7 +10886,16 @@ the numbers of cells across batches.") r-stringr r-summarizedexperiment)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("js-jquery-sticky-kit" + ,(origin + (method url-fetch) + (uri + "https://cdn.jsdelivr.net/gh/leafo/[email protected]/jquery.sticky-kit.js") + (sha256 + (base32 + "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g")))) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -11424,14 +11583,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.1") + (version "2.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) + "0snsvyy8d85panizm848mrmjpgyc06iqp39d19rny3fphq3adwn5")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -11526,14 +11685,14 @@ surface of a flowcell.") (define-public r-mutoss (package (name "r-mutoss") - (version "0.1-12") + (version "0.1-13") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 - "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) + "0hgi9wpy3ai23dk6cdba6r118vvmgw210racsg3n1p24rv6ny3xn")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs @@ -11772,14 +11931,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.1") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) + "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -11934,14 +12093,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.6.0") + (version "4.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) + "017wqd1nwcrhbpzvhcqc3if0n084dspq7y3fbc5dnik6yi04q0dg")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -11972,13 +12131,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.1") + (version "2.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) + "03flqixy6flaqynpaf3nz42kwf71v53wxs5vywj3bqmninzywmbk")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12401,12 +12560,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.12.0") + (version "2.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) + (base32 "073xv26yaksqa0j2vyqf8ak5yqsxg5s86izdlmlwdidnxdnd16si")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -13463,14 +13622,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) + "0cbm6q4v9ddyx4gnw2p47ssyhnmjfxahvzbzwjzn0my3ixssy0aj")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -13578,14 +13737,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.2") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) + "0d7qsdjry5avflrvgjj287xqn9dr54pqiqvpgywzdmdwn82m0dfp")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -14018,14 +14177,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.2") + (version "2.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) + "0lhmva8yghlbb44h1fvbcqfp8zvdn4pd4nwyd2drh6b271f8qjdd")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -14775,14 +14934,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.16.0") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) + "1gf359x6lvm3kc4mlsh7vxf8lmvhp080fi0cksvb4mcypafp67cv")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -14842,14 +15001,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) + "1i954hn7xyajpkg4fks04jd86flcmy2326nzpmxgy8h69jkzdc8q")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -15430,14 +15589,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.4") + (version "1.28.7") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1ii4r0c76b7rnisy4qba2cp5686j73s6b3s6pj66w91wq65dykpd")))) + "0iv5c5p0g4axhanc62mmk0c43qcwdsxzslxh5qdck0v1kb7bd1d9")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -16324,13 +16483,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.34.2") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) + "00z2l5jnc028bmd3rl3qmgkd6k1mfa4p68kls34mkn29ic9ls22m")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -16399,13 +16558,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.2") + (version "1.66.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y")))) + "0ddxz7a8csf1l4srnjcgg5ps00fkcbv99y5wa0yrl6p9zr2d61qy")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -16598,16 +16757,50 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) + "0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf")) + (snippet + '(for-each delete-file + '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" + "inst/htmlwidgets/lib/bioc_explore/d3.v3.min.js" + "inst/htmlwidgets/lib/bioc_explore/jquery-2.2.4.min.js" + "inst/htmlwidgets/lib/bioc_explore/underscore-min.js"))))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/bioc_explore" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-bootstrap") + "bootstrap.min.js") + (,(assoc-ref inputs "js-d3") + "d3.v3.min.js") + (,(assoc-ref inputs "js-jquery") + "jquery-2.2.4.min.js") + (,(search-input-file inputs "/underscore.js") + "underscore-min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) (propagated-inputs (list r-biocfilecache r-biocmanager @@ -16631,7 +16824,40 @@ gene selection, testing relationships, and so on.") r-tibble r-xml2)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-bootstrap" + ,(origin + (method url-fetch) + (uri + "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.6/dist/js/bootstrap.js") + (sha256 + (base32 + "07fm28xbkb7a5n7zgmfxgbl2g5j010r4gvc54y79v1f119s3kz6y")))) + ("js-d3" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-2.2.4.js") + (sha256 + (base32 + "18m6qmmsm3knvybf6gpwmwiasi05y98gcpb364if8qh94gv90gl9")))) + ("js-underscore" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jashkenas/underscore") + (commit "1.8.3"))) + (file-name (git-file-name "underscorejs" "1.8.3")) + (sha256 + (base32 + "1r54smxpl3c6jg6py29xjc2l1z49rlm1h48vr9i57wvnkbnbl0h3")))))) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -17007,13 +17233,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.1") + (version "0.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) + "131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -17112,13 +17338,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) + "0kc1xzq03kz548rfinxhc7gxm6021502b6v7bg2har0aq4vx79ml")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (inputs (list zlib)) @@ -17131,7 +17357,6 @@ objects from the @code{graph} package.") r-matrix r-matrixstats r-qvalue - r-rcpp r-s4vectors r-singlecellexperiment r-summarizedexperiment @@ -17517,13 +17742,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) + (base32 "034in81lsdxa8j1na2zymck2y67235qprin8hak3dwa7lwzbm12z")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -18947,14 +19172,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) + "0h1cwir6m3zg728vdxxz03rfwysw92m9djdfj0vayixli2j4xz5a")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments |