diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 489 |
1 files changed, 294 insertions, 195 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3419900f5..f38b787bdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -290,13 +290,13 @@ even help to identify disease associations that are not obvious.") (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") - (version "3.12.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 - (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) + (base32 "12lqv06n49lwczv5l4h5h6lbfbcqyg9j4csffcdx495scmhc06mc")))) (properties `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) @@ -317,7 +317,7 @@ analysis.") (define-public r-org-bt-eg-db (package (name "r-org-bt-eg-db") - (version "3.13.0") + (version "3.18.0") (source (origin (method url-fetch) @@ -327,7 +327,7 @@ analysis.") 'annotation)) (sha256 (base32 - "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi")))) + "0fgrpjfrsw837ay9cq3wd6gp6sxvwjc7r9spfs4m89vqs2xb0bfc")))) (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs @@ -342,14 +342,14 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-sc-sgd-db (package (name "r-org-sc-sgd-db") - (version "3.17.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Sc.sgd.db" version 'annotation)) (sha256 - (base32 "1anxk5sgzgkdk4n1c7gjyzy56wa2bkifghs9m1mh82l95kyvk2ig")))) + (base32 "15ngfqimrjpn2fxzngj5m3pvqivbq65010qdx33xs32ax48z6p2r")))) (properties `((upstream-name . "org.Sc.sgd.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) @@ -391,14 +391,14 @@ Mapping50K_Xba240 (pd.mapping50k.xba240).") (define-public r-reactome-db (package (name "r-reactome-db") - (version "1.70.0") + (version "1.86.2") (source (origin (method url-fetch) (uri (bioconductor-uri "reactome.db" version 'annotation)) (sha256 (base32 - "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) + "02p8ihds0hpcfj5mib0ifql9404svlavfyj36c15jzmbci0rnc8c")))) (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs @@ -739,14 +739,14 @@ default." ) (define-public r-bsgenome-mmusculus-ucsc-mm10 (package (name "r-bsgenome-mmusculus-ucsc-mm10") - (version "1.4.0") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" version 'annotation)) (sha256 (base32 - "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) + "1vprkywr72nqf847vzmgymylcdb45g4hy30fwx6fzwddkyzh5xnw")))) (properties `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) @@ -764,13 +764,13 @@ in Biostrings objects.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "1.2.0") + (version "1.2.11") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) (sha256 (base32 - "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) + "1hkvcrp4a2g3yl1h4k5zzj5fhp3d9a1amyn19zr62q9fhj3y47ri")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -783,13 +783,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-go-db (package (name "r-go-db") - (version "3.7.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GO.db" version 'annotation)) (sha256 (base32 - "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) + "0znqa724jvrw2xx696n48lx83kzhivfr7fc9awzgm7nigwg3907m")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -884,7 +884,7 @@ from several related annotation packages.") (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 (package (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) @@ -893,7 +893,7 @@ from several related annotation packages.") version 'annotation)) (sha256 (base32 - "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) + "1272n72fvj4agszd9cv8l9h9qr2pzmd0rbvdz83x7x03cdddf9rn")))) (properties `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) @@ -954,13 +954,13 @@ data.") (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.7.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) (sha256 (base32 - "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) + "1fsbrbby6ka2xdsbp8b10nid99w6lkvb7pyn8gv3dsn8p9p6mc5q")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) @@ -976,13 +976,13 @@ annotations for the genome of the model worm Caenorhabditis elegans.") (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") - (version "3.7.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) (sha256 (base32 - "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) + "1n0rwynw3nl4js104295kff0jk8jwymjk8imm9di6dy6b9s3qsa6")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) @@ -998,13 +998,13 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") (define-public r-org-dr-eg-db (package (name "r-org-dr-eg-db") - (version "3.7.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) (sha256 (base32 - "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) + "1kk5jgbzcqhgwf5p4mpxswqhr9rkirm3fb7maflk61zcn6fs56zc")))) (properties `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) @@ -1042,13 +1042,13 @@ on mapping using Entrez Gene identifiers.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.7.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) (sha256 (base32 - "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) + "0i35dfllh8wf7b61ajf33gvclzg3znyx3cgp30vs3hm8ys3nras1")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) @@ -1088,18 +1088,18 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") (define-public r-bsgenome-hsapiens-ucsc-hg38 (package (name "r-bsgenome-hsapiens-ucsc-hg38") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" version 'annotation)) (sha256 - (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2")))) + (base32 "0lp94r9dsx8sl1ifysavgjf4aamhjc4n71zif5jyfnwmzpj7g4ml")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs - (list r-bsgenome)) + (list r-bsgenome r-genomeinfodb)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") @@ -1299,13 +1299,13 @@ track. The database is exposed as a @code{TxDb} object.") (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") - (version "3.15.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 - (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879")))) + (base32 "0ak6acjll2djamakpn60ks47lfs2y0r8xwhjazj6fvch34xkc2d5")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) @@ -1487,13 +1487,13 @@ data (chip hgu133plus2) assembled using data from public repositories.") (define-public r-pfam-db (package (name "r-pfam-db") - (version "3.15.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 - (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7")))) + (base32 "15m7qfvz53jkdmx90y7rvy62myr4y3hdy414yqi0w3ch32vy78nr")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs @@ -1574,12 +1574,12 @@ All datasets are restricted to protein coding genes.") (define-public r-adductdata (package (name "r-adductdata") - (version "1.12.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductData" version 'experiment)) (sha256 - (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48")))) + (base32 "16c79wy55p4ryglxph80dibfm1ni8c5yfk6fnmq064ihw4zwcld5")))) (properties `((upstream-name . "adductData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-experimenthub)) @@ -1595,12 +1595,12 @@ albumin} (HSA).") (define-public r-aneufinderdata (package (name "r-aneufinderdata") - (version "1.24.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinderData" version 'experiment)) (sha256 - (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7")))) + (base32 "03kp8qkqy2wph7lbzawgnh83qjm31ih1jp986qwphfhkfk125wg0")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/AneuFinderData/") (synopsis "Data package for @code{AneuFinder}") @@ -1611,12 +1611,12 @@ demonstration purposes in the @code{AneuFinder} package.") (define-public r-arrmdata (package (name "r-arrmdata") - (version "1.32.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmData" version 'experiment)) (sha256 - (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p")))) + (base32 "0hlhc7kvw9n1bnbzingd1475qwivpx64sccnigdij8xdcm1mb4s7")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) @@ -1630,14 +1630,14 @@ from Illumina 450k methylation arrays.") (define-public r-bcellviper (package (name "r-bcellviper") - (version "1.34.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bcellViper" version 'experiment)) (sha256 (base32 - "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm")))) + "1q9ig5z03flq57nrhwnk6gdz4kamjmpwdfifwvnhac3l3f5z828h")))) (properties `((upstream-name . "bcellViper"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1653,14 +1653,14 @@ dataset for the examples in package viper.") (define-public r-bladderbatch (package (name "r-bladderbatch") - (version "1.34.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bladderbatch" version 'experiment)) (sha256 (base32 - "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k")))) + "19dgvdbxsswy1fl68wwf4ifplppm1blzjw1dr06mz0yjq80a7rvl")))) (properties `((upstream-name . "bladderbatch"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1671,21 +1671,59 @@ dataset for the examples in package viper.") 5 batches. The data are used as an illustrative example for the sva package.") (license license:artistic2.0))) +(define-public r-bodymaprat + (package + (name "r-bodymaprat") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bodymapRat" version + 'experiment)) + (sha256 + (base32 "1sfq6vxkb68l0q5qbnpm3fi53k4q9a890bv2ff9c6clhc42wx3h6")))) + (properties `((upstream-name . "bodymapRat"))) + (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-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/bodymapRat") + (synopsis "Experimental dataset from the rat BodyMap project") + (description + "This package contains a @code{SummarizedExperiment} from the Yu et +al. (2013) paper that performed the rat @code{BodyMap} across 11 organs and 4 +developmental stages. Raw FASTQ files were downloaded and mapped using +STAR. Data is available on @code{ExperimentHub} as a data package.") + (license license:cc-by4.0))) + (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") - (version "1.10.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteerData" version 'experiment)) (sha256 - (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw")))) + (base32 "1wqdj1499psnf9y816k05m6h38yfsin4rwzqm1209ddxza6jbw1x")))) (properties `((upstream-name . "biscuiteerData"))) (build-system r-build-system) (propagated-inputs - (list r-annotationhub r-curl r-experimenthub)) + (list r-annotationhub r-curl r-experimenthub r-genomicranges)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biscuiteerData") (synopsis "Data package for Biscuiteer") @@ -1697,13 +1735,13 @@ biscuiteer.") (define-public r-breakpointrdata (package (name "r-breakpointrdata") - (version "1.16.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointRdata" version 'experiment)) (sha256 (base32 - "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn")))) + "13w9vp436akpnywhsr6kz763c2yakrvpyiplggfb6w50wi2xm5xj")))) (properties `((upstream-name . "breakpointRdata"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1737,13 +1775,13 @@ cancer study published in Wang et al. 2005 and Minn et al 2007.") (define-public r-celldex (package (name "r-celldex") - (version "1.6.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "celldex" version 'experiment)) (sha256 - (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10")))) + (base32 "1ckjdmiw9g1wdswijy3dvamv3kqi11j8b8p9dgr1yv5q2lfjbnwl")))) (properties `((upstream-name . "celldex"))) (build-system r-build-system) (propagated-inputs @@ -1766,13 +1804,13 @@ single-cell data or deconvolution of bulk RNA-seq.") (define-public r-champdata (package (name "r-champdata") - (version "2.30.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMPdata" version 'experiment)) (sha256 (base32 - "0rz762szfl02h4d3dj7ckd41ji9mdsja8nxqw6fl086z337041zw")))) + "175vsg2bh578fdrdchcma5q3jq7cfxa8b7g8954xv6fxrwcj0ffz")))) (properties `((upstream-name . "ChAMPdata"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-genomicranges)) @@ -1786,13 +1824,13 @@ and blood controls for CNA analysis.") (define-public r-chromstardata (package (name "r-chromstardata") - (version "1.22.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaRData" version 'experiment)) (sha256 - (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1")))) + (base32 "13xrdr9xrfysh714q4p00pgvwr6ryhvd3jinfqr1gb27s7bdvsi6")))) (properties `((upstream-name . "chromstaRData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/chromstaRData/") @@ -1805,13 +1843,13 @@ chromstaR package.") (define-public r-copyhelper (package (name "r-copyhelper") - (version "1.28.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) (sha256 - (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1")))) + (base32 "1zfsxi65lln93fb87l6fgp7vxldb4fvnf95h91dl424xyq6qjp1h")))) (properties `((upstream-name . "CopyhelpeR"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/CopyhelpeR/") @@ -1828,14 +1866,14 @@ GenomicRanges Bioconductor package.") (define-public r-flowsorted-blood-450k (package (name "r-flowsorted-blood-450k") - (version "1.36.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.450k" version 'experiment)) (sha256 (base32 - "1ha9qsp5g3g2yhnk574x6xhg95bb29ywvmg3ns1c50z69v6wbraq")))) + "08xli4a24kkyy5q1ka0vyrpk11yfkyp0gxbs0k8khycppsq9s9sn")))) (properties `((upstream-name . "FlowSorted.Blood.450k"))) (build-system r-build-system) (propagated-inputs (list r-minfi)) @@ -1851,14 +1889,14 @@ associated with cell type.") (define-public r-flowsorted-blood-epic (package (name "r-flowsorted-blood-epic") - (version "2.2.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.EPIC" version 'experiment)) (sha256 (base32 - "1vybj69jxnirqg6ik03q3pb1vv23z8mir7wpi2ys7iljf5ixzgl1")))) + "0vfx1kpy02640nkkkpksisznybv0xb6jkvvkwsybsggcr2rdkl89")))) (properties `((upstream-name . "FlowSorted.Blood.EPIC"))) (build-system r-build-system) (propagated-inputs @@ -1885,18 +1923,18 @@ https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.") (define-public r-genelendatabase (package (name "r-genelendatabase") - (version "1.32.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (sha256 - (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz")))) + (base32 "0skycixz0qbm8cs10kgrkl1ab1qh0mz8641mf5194y839m81d060")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs - (list r-rtracklayer r-genomicfeatures)) + (list r-genomicfeatures r-rtracklayer)) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description @@ -1907,13 +1945,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.28.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomationData" version 'experiment)) (sha256 - (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh")))) + (base32 "044q01dbcd34lxgwpg76yk0msvx7gpiibiqxp6fr9jswq6izrzq7")))) (properties `((upstream-name . "genomationData"))) (build-system r-build-system) @@ -1933,13 +1971,13 @@ downloaded from Encode.") (define-public r-hdcytodata (package (name "r-hdcytodata") - (version "1.18.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDCytoData" version 'experiment)) (sha256 (base32 - "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc")))) + "1xqwkwxaaj5yylx9pzvka8pj9gxg1z4g23d2sralcvqzcz7q13zn")))) (properties `((upstream-name . "HDCytoData"))) (build-system r-build-system) (arguments @@ -1974,14 +2012,14 @@ includes channel names, protein marker names, and protein marker classes.") (define-public r-illumina450probevariants-db (package (name "r-illumina450probevariants-db") - (version "1.34.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Illumina450ProbeVariants.db" version 'experiment)) (sha256 (base32 - "1c1iqxi17s1a1sa1vab2ma7pjq1dxal7ibsiahj66ys0pa4sm42p")))) + "1h0qcdmyd22x5y5iwi1w89ppb1k3nb2awwim1lcxgdinab8km52b")))) (properties `((upstream-name . "Illumina450ProbeVariants.db"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db") @@ -1996,13 +2034,13 @@ European).") (define-public r-italicsdata (package (name "r-italicsdata") - (version "2.36.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICSData" version 'experiment)) (sha256 - (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw")))) + (base32 "0fzx2qqykma2r2ds53wik4kb9a0wvybr63vf34s91731k21mgsqn")))) (properties `((upstream-name . "ITALICSData"))) (build-system r-build-system) (home-page "http://bioinfo.curie.fr") @@ -2034,14 +2072,14 @@ please use the package TFBSTools.") (define-public r-macrophage (package (name "r-macrophage") - (version "1.12.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "macrophage" version 'experiment)) (sha256 (base32 - "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms")))) + "10d69v34fhxfy4nhw8h50j4q5kblm032cmjnparxm5gm7ksiqwxy")))) (properties `((upstream-name . "macrophage"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2085,14 +2123,14 @@ with different methylation clocks.") (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MouseGastrulationData" version 'experiment)) (sha256 (base32 - "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17")))) + "0m03wrqgfhlyc0rmjjcj8b9gcc2rv644hffnff3j1bnkjg5rldi0")))) (properties `((upstream-name . "MouseGastrulationData"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -2116,13 +2154,13 @@ timecourse of mouse gastrulation and early organogenesis.") (define-public r-minfidata (package (name "r-minfidata") - (version "0.44.0") + (version "0.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfiData" version 'experiment)) (sha256 (base32 - "15s3kc629m2c78vkidmp6kcc28sn1wzjzrxazmd8z7x8cdad3q4g")))) + "12lhyv3zb8vps7v61zfm8sz4r18rpgphgy7nvdpj48dj3awdnpw8")))) (properties `((upstream-name . "minfiData"))) (build-system r-build-system) (propagated-inputs @@ -2139,13 +2177,13 @@ methylation arrays.") (define-public r-msdata (package (name "r-msdata") - (version "0.36.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msdata" version 'experiment)) (sha256 - (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691")))) + (base32 "1jm1zjqzkd0vy8ww0k0y1fgs6i9vkg7ir6dyga001n170g11vfzr")))) (properties `((upstream-name . "msdata"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/msdata") @@ -2196,14 +2234,14 @@ containers.") (define-public r-msigdb (package (name "r-msigdb") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msigdb" version 'experiment)) (sha256 (base32 - "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby")))) + "1fzgq31n059zhlkny3rfwfnriz81q9brk14r5yx2zhizlv8jcais")))) (properties `((upstream-name . "msigdb"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -2228,13 +2266,13 @@ along with the gene set in the @code{GeneSet} class object.") (define-public r-pasilla (package (name "r-pasilla") - (version "1.24.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 - (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib")))) + (base32 "0dga4bb7qjigy1m1yp4bs4frwynjqfy3dnnylx4maai9x2zlynd0")))) (build-system r-build-system) (propagated-inputs (list r-dexseq)) (native-inputs (list r-knitr)) @@ -2249,13 +2287,13 @@ by Brooks et al., Genome Research 2011.") (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") - (version "1.16.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) (sha256 - (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v")))) + (base32 "1nf6jsjvy3qacwz0dl5jc9h87xhj9q73b0g49c2yrxvv1dhayq0i")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) @@ -2278,13 +2316,13 @@ resulting in a complete gene expression profile for each cell.") (define-public r-all (package (name "r-all") - (version "1.38.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 - (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z")))) + (base32 "1ny5xv338a91gc88a1y5rrd27iawrrlmxhkidvc7xdsbrwd4flkc")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs @@ -2302,13 +2340,13 @@ the form of an @code{exprSet} object.") (define-public r-affydata (package (name "r-affydata") - (version "1.44.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 - (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp")))) + (base32 "1p9gqv8xnakwhf4sani09krlrq6qs4gr8yfjmi8g3s1zq4d32h1k")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs @@ -2324,13 +2362,13 @@ package @code{affy}.") (define-public r-gagedata (package (name "r-gagedata") - (version "2.34.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 - (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9")))) + (base32 "13g8hzkh34c0my75xnxdffa1d67xvn9hn592s25m18400lgsfif0")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") @@ -2350,13 +2388,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.18.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr")))) + (base32 "0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -2383,14 +2421,14 @@ across the entire multi-'omics experiment.") (define-public r-parathyroidse (package (name "r-parathyroidse") - (version "1.34.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parathyroidSE" version 'experiment)) (sha256 (base32 - "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16")))) + "0lv7wlbdi05a3l4pv8x4cnc6jzqk1gb82rpmj1cv0nsq7gqhqscv")))) (properties `((upstream-name . "parathyroidSE"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -2407,14 +2445,14 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro (define-public r-sesamedata (package (name "r-sesamedata") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesameData" version 'experiment)) (sha256 (base32 - "1fvxs5n6bj2j0k3vgnaiksshkaxw7fmx6k22rjd3fsqg3cz60fm6")))) + "0a5xchdnlw9ixafk8p3ny58yqv74ba9j4z2sdyp990rbaqrx1gjw")))) (properties `((upstream-name . "sesameData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub @@ -2441,13 +2479,13 @@ the @code{HorvathMethylChip40} (Mammal40) array.") (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") - (version "1.16.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) (sha256 - (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g")))) + (base32 "04fmnqa95rb2lgflcg3d7kbz9jj990r9hlxwlhhzb79dv9wd1mfa")))) (properties `((upstream-name . "TCGAbiolinksGUI.data"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2460,14 +2498,14 @@ TCGAbiolinksGUI package.") (define-public r-tximportdata (package (name "r-tximportdata") - (version "1.24.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximportData" version 'experiment)) (sha256 (base32 - "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy")))) + "0ksmg3gblkqzz40pzm35y6wghjmszrimdx7bxhq5jv4piqwii0hg")))) (properties `((upstream-name . "tximportData"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3318,13 +3356,13 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.18.2") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "1q0ca3pagqzj12kah79jg4py3ibz7qsdl975r2mxhphqwj76gnh8")))) + "0j8fa5cr6s20bgw7v62by61q7nk8iw64v4wshwbd2cc36gr7s3c8")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs @@ -3375,13 +3413,13 @@ to understand their data better and discover new insights.") (define-public r-annotationhubdata (package (name "r-annotationhubdata") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHubData" version)) (sha256 - (base32 "0jkz65z7l9vaxid6vpsr4rdavarkayfrgkybzhwf9va82jsnkd3z")))) + (base32 "09x2njf32lvj2irpjffjn2bsh42zkchirb7779xfyh745iis57mm")))) (properties `((upstream-name . "AnnotationHubData"))) (build-system r-build-system) (arguments @@ -3426,13 +3464,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "06n0as71m3dfbnzjfq8f1s0r40w4flc8am7zb0293c1037clmcig")))) + "1vfriymy1v3mxahfdf4sd6rawi0qy7vzxrymi852w49fmy54bgp7")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs @@ -3751,13 +3789,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.22.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "08vkkfccfq8j4hanxsmjx5657kkw4qcp46qfhqvp1sd6wym69wzw")))) + "0yal8lbillhj3zi2rcdk7k9r748jxm3196z54y1674qxzpvp24rk")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs @@ -6238,23 +6276,22 @@ Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.") (define-public r-nmf (package (name "r-nmf") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "1h1fpjnj6vjvi9ygxpfxs8k5bhly0aflr54zj88khgzkylp5ci4d")))) + "1y9y7xpfd9y8j5b8s2x5g61455ilpgqpdhrirpz58xjarbph4hxg")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs - (list r-cluster - r-codetools - r-biobase + (list r-biobase r-biocmanager - r-bigmemory ; suggested - r-synchronicity ; suggested + r-bigmemory ;suggested + r-cluster + r-codetools r-colorspace r-digest r-doparallel @@ -6265,7 +6302,8 @@ Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.") r-registry r-reshape2 r-rngtools - r-stringr)) + r-stringr + r-synchronicity)) ;suggested (native-inputs (list r-knitr)) (home-page "https://renozao.github.io/NMF") @@ -6725,13 +6763,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.58.0") + (version "2.58.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1m6c6m9z0d1k6s2q0ikd78ahcq72gzqnhlprdn0xvkjxrgh1i2lf")))) + "03hl64j7fknw4gzw9w653zzw5gdxyi7r95vxr5ksz0m3n9xdv124")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -6861,13 +6899,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.70.1") + (version "2.70.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "198y36yfkncsp4sw00ij8cal45al67f9nx84bbszhygaq0jh504y")))) + "0lmaknlw3mk946h26davr9cz5xpzjp0c8qjxbr7drj8b2cjfm66a")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6932,13 +6970,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.70.1") + (version "1.70.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1bdrh1kp7ihnlyvgdvwdzly69l9zy5rr09gizm0l59zy4kh59nih")))) + "02qrqg7lfisj44gvlfn1gkhxxjqdh11q28inxggfpcda9b67j61d")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7173,13 +7211,13 @@ self-defined annotation graphics.") (define-public r-conos (package (name "r-conos") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "conos" version)) (sha256 - (base32 "1wdhb3jxh4id6xaghawzip8s264g9jxp4i5xy7jfhi67yfxszx6w")))) + (base32 "01d2knwyf0g2pvqq3dy5vhf0i7mc5f7rzg3a7cbglsw3l9irsixv")))) (properties `((upstream-name . "conos"))) (build-system r-build-system) (propagated-inputs @@ -7441,13 +7479,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "17ks6bbhv8iw8grzlkibgqmwggrqp5hikg1p49m4a6b6bayillv2")))) + "0qyiq6azknjqim0hjy5xw5gvs5jyczx29vcs95dwsfk92sygdps0")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -7525,13 +7563,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.9") + (version "4.0.16") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1jdpvswcnspiypk9c2wq01cgcv1l5061q9h8gc5khhk9jlyv44bg")))) + "0jflbh1wsszz98y0y294g69mm81fwwxfbhpi3kmdncin8bwf8ifi")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7843,13 +7881,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.38.5") + (version "1.38.6") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "17w5zrvpk2x0sc55xfkbn9krphg4aszmvwmj1qfsf1bdrazfpwic")))) + "0z8wkv5jhx8wr6idnakm26lhhk4ssj6ivbb7hfbzhkajcbnnf7mq")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7934,13 +7972,13 @@ Commons RESTful service.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.54.1") + (version "1.54.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1b2rx16l7zd4lisqssbkcwi534s7m7h1w6k72km6c835x2cdxfs4")))) + "1b78fss1nfyph6b7pv3ss6iv6r2qgrmx4klxvq8waz2nxvikxdl5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8439,14 +8477,14 @@ be calculated to search in MS peak lists.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1h0hzs4f4mmnpi436dgib9lakljacznkyyssy7c4mdd419431aq2")))) + "089b5amwxwac6wvdnndy9inc218919q9dz9x58i2cp7il18vjd0c")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -9943,13 +9981,13 @@ analysis of TCR repertoire libraries based on theoretical model fits.") (define-public r-pscbs (package (name "r-pscbs") - (version "0.66.0") + (version "0.67.0") (source (origin (method url-fetch) (uri (cran-uri "PSCBS" version)) (sha256 - (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (base32 "1gnd2nkh587dqpnbk5fsai7hx261vm405550rhlxffvs366x3596")))) (properties `((upstream-name . "PSCBS"))) (build-system r-build-system) (arguments @@ -9980,6 +10018,68 @@ data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (license license:gpl2+))) +(define-public r-protgear + (package + (name "r-protgear") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "protGear" version)) + (sha256 + (base32 "0r8md32vxjzarjldr9vsh3k0ms4zgqm9c7pp2flanbyinnqlfnxv")))) + (properties `((upstream-name . "protGear"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed by styler for writing to caches. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs (list r-biobase + r-data-table + r-dplyr + r-factoextra + r-factominer + r-flexdashboard + r-genefilter + r-ggally + r-ggplot2 + r-ggpubr + r-gtools + r-htmltools + r-kendall + r-knitr + r-limma + r-magrittr + r-mass + r-pheatmap + r-plotly + r-plyr + r-purrr + r-readr + r-remotes + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-styler + r-tibble + r-tidyr + r-vsn)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/Keniajin/protGear") + (synopsis + "Protein micro array data management and interactive visualization") + (description + "This package provides a generic three-step pre-processing package for +protein microarray data. This package contains different data pre-processing +procedures to allow comparison of their performance. These steps are +background correction, the coefficient of variation (CV) based filtering, +batch correction and normalization.") + (license license:gpl3))) + (define-public r-protgenerics (package (name "r-protgenerics") @@ -10026,13 +10126,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.28.2") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "19ildsck3g8v4w0g2f473sb8hyhn4avprdi78fim0prva5f9nqnv")))) + "1d9icr17xwdmgm6b8ihrwxsg1fp342c2p9f8yqdjm2y52z88gmpd")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -10048,7 +10148,6 @@ the graph algorithms contained in the Boost library.") r-genomicfeatures r-genomicranges r-ggplot2 - r-ggseqlogo r-gprofiler2 r-iranges r-knitr @@ -10062,7 +10161,7 @@ the graph algorithms contained in the Boost library.") r-rsqlite r-rtracklayer r-s4vectors - pandoc)) + r-seqlogo)) (native-inputs (list r-knitr)) (synopsis "RNA-centric annotation system") @@ -10851,13 +10950,13 @@ single-cell RNA-seq.") (define-public r-seqarray (package (name "r-seqarray") - (version "1.42.0") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SeqArray" version)) (sha256 (base32 - "0zs60yh3x6kgy6izn11d400vw59ww2w6bmhg6fw5ijinknyr3ixc")))) + "1bwqyvvfwwscznwi1bm4wh2pqf0fmq68g7siwbbw5ypj087ibnnm")))) (properties `((upstream-name . "SeqArray"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -11375,14 +11474,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "0pqdl0v16q90ffxla34rp07mq0if1q9izpbimfnq0rx7633mk95v")))) + "178v5r0nck9ils5k7hj92x7z1xk5zq6zyc78wqnz7s3shbnq9ld7")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -12752,18 +12851,18 @@ expressed genes in DNA microarray experiments.") (define-public r-ggm (package (name "r-ggm") - (version "2.5") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggm" version)) (sha256 (base32 - "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) + "1bp00m93mrx33gpd36qnrxx60y17aimlh6bd36cqyh6vpf0vpfvg")))) (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs - (list r-graph r-igraph)) + (list r-biocmanager r-graph r-igraph)) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description @@ -12930,14 +13029,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.36.0") + (version "3.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "012hhakhk81qk1hi4igfa4vji678gmyvdxi05z9mdsx721lwwy2i")))) + "1jmg958v8ai9v3mpizj24nc0vsl564inndm0irflprs1ky90k8vl")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -13433,13 +13532,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.14.0") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "1qc3f1spzkcjk95b07jpxgrjiwmlamwwx6mlhml4lgzy5qby7dpw")))) + "0lbsavr9mhka8s7i056h4jjb1v36v3sshrhdz74n8qadm7fy59l5")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -15517,18 +15616,18 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.28.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "10jhjzgf10w9cmr97qzc3mqvgvgx9h7pqk7zkkqwhg7anv6wa788")))) + "0p8368ia4ib61m1p8apk2d21lhdi62rfg04zl4190w6xv87k49xx")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-go-db r-rcpp r-rlang)) + (list r-annotationdbi r-go-db r-rcpp r-rlang r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") @@ -16107,14 +16206,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1hdqnipg326z2k7vs6sc1brc9lvvhmr2l6cjp4f9a205g4q7r9rr")))) + "0sibsmn7ma2imhfn2pn1fvy6hinzlmsczmx944fzg0aj1lpjcdqr")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -16500,14 +16599,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.22.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1baa3aabkhmwq66xkzf4jk5nz85kkx1ks0mqc91s2ra9916wj6cd")))) + "004483q584530mh5nb28ppa8wllkd639n9yyw309acs2s4rc7saa")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -17953,14 +18052,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0bhq8q3dch09r3digf3snfvhyj6w7j1qqw8gl28b29in8azg6v4d")))) + "0rgfl1kmgf2f0lpj2fzgjvdm5d7swp9wz86jl8q9mydw6z49nxz8")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -18211,14 +18310,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "11aic1nzlw0gdpcpmky5jzljxgxcrimi29f0zl3yjvgb48qa88bd")))) + "1g6qxzvzn1gnmqba150lj9nb6wlrdpzkc61l77d3fkzaf0q1h1n7")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -18427,14 +18526,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.14.1") + (version "4.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0sbixbq99kmhh0ppdid1hqhb75yxb6gsm5pdz75y67i3pgwrv1sj")))) + "0rbhpvnx71djy893cb1b1qywm5aq8ad8rxjd0lqkylp13w7zv0g6")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -18474,14 +18573,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.14.0") + (version "4.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1f7qawn9wb8221npnmmygmvi4w1rq5lb74j3vmfzcak5kyga5xck")))) + "1q4m6arasq60w0x24qjxbfckfgcpfk428fca733i0q2mgv1mll05")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -19408,14 +19507,14 @@ populations, splice site strength, conservation, etc.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.32.2") + (version "1.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0cmcg39a5939y517vhvwanqh1fwzyx6pbq47nc5cpswf7pn9cv5x")))) + "1yrss51gwg73rlva0xhk34md0cx43h2j4vfk0z2hzchr2r1amzmc")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -19797,14 +19896,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.68.0") + (version "1.68.3") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0v85i0lwmxq5yq9ygfzljgy8fsflqq1p53rq8aasnndd6gsm8ld2")))) + "1a3hq2i1mxf6dpkk82b6y88q5fcjbqpdcxqplkfp5d2slzsqc3jp")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -20418,13 +20517,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "11d67dfwxc34n7yzpz58ficjk7sxnbxrajhnqlcxvsifgmybkb4d")))) + "1pkh7b27ynzpdfvyzqg36jm885r5lf2zw9rppdpj31rcv1640s0k")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -20436,8 +20535,9 @@ monograph.") r-callr r-codetools r-graph - r-httr + r-httr2 r-knitr + r-rvest r-stringdist)) (native-inputs (list r-knitr)) @@ -20837,14 +20937,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "0sk4kmvl86xm85dqaf8gvii0qavyycyn2qp0v6dmfcjqai528v2x")))) + "1qmi6b0hrfzj7ixcbxlsxyy3qg7d2qrq8jcjrjrgfyrgcfws46qd")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -21431,14 +21531,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0p52n96mydqszpq1ysmbh5xs4n4icqsd0gbxl5wpkcwvvhxliw8b")))) + "17cjjlgbp5kj0cpjm6915wy4cm6h5wl6d59j4na1s6kvgxx95qd0")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -21463,14 +21563,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.24.1") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0lb5dkzfnfvxwrk8s9vzfjp8ab1sbr7b22jnzg41hgmpysi7dswh")) + "0b2g57dxvzmnq6dig4dz7cy8lpy3q7fih5q643i5xjcds2cj6lk5")) (modules '((guix build utils))) (snippet '(begin @@ -21531,11 +21631,10 @@ block processing.") (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - (list hdf5-1.10 r-biocstyle r-stringr zlib)) + (list hdf5-1.10 zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -21545,14 +21644,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1yixv6vs1q2k4vx17bq4nar3g4v2076i5dq77gh63mlka46qr3g2")))) + "1kz8jn3kaqrhvk1dd92l7w45mmwabcqb0508fv4i4w307ja8xk2l")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray)) @@ -21987,14 +22086,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.30.1") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "02840dw467dqdg09abxlzps1l1xnzhinlmpmqgfsq70pzqf7jywk")))) + "06b454ydd8n8xbswxf1hacm3g2nr0ik0gg08pr7crgnsm0r3vpvs")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -22030,13 +22129,13 @@ variable and significantly correlated genes.") (define-public r-sparsearray (package (name "r-sparsearray") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (bioconductor-uri "SparseArray" version)) (sha256 - (base32 "19cy1nmmi65fxh012ymgp1kg112yl1m0khcs4y034p5iwlfv7fp6")))) + (base32 "0gz1j8g020bp88i5idrhj9qrixgar3wvxxna46ds60q6d8lsn4vi")))) (properties `((upstream-name . "SparseArray"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -23472,14 +23571,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "0fi3211p7fzab0bw2zqkc7gnqzpi24sf8655wghaw3yg9g39ksdg")))) + "0hmx2jpfmjv87mp99mzbbzg00m6arpkpc5prkfav065iwjqbqnpd")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -23873,14 +23972,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0pq5fiacb2x8l5jk3p6bnha9bcwg91grpklgx2nirrlwwr80gf2h")))) + "0dxn4pijr6gsqybl8x3ix1xydizg7gzfp72risk37zc5i4xk2lca")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -24194,14 +24293,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "0z53vh5qirkyn7yw3g2m2kj6dzii96l81vc8j59n2dl7p602l9a2")))) + "10ps9k5cp2adpx91g23gc9hl1qzzax5w1mxjcjaii7knkh70cz3p")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -24462,14 +24561,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.20.2") + (version "1.20.3") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1i6d1kw8wqcdzdhzlix29jl5ka8p54nb4b5zyn9ca356nkxf755q")))) + "0hlx5kvhspc62p68gz53n0scwji3zvfv915fm8rzw3l8h2hjh3y7")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |