diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 890 |
1 files changed, 717 insertions, 173 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d82a73ac51..a54c9006a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -55,6 +55,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages maths) + #:use-module (gnu packages ncurses) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #:use-module (gnu packages perl) @@ -105,6 +106,26 @@ Only the AGAPS and AMB masks are \"active\" by default. The sequences are store in @code{MaskedDNAString} objects.") (license license:artistic2.0))) +(define-public r-ensdb-hsapiens-v79 + (package + (name "r-ensdb-hsapiens-v79") + (version "2.99.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EnsDb.Hsapiens.v79" version + 'annotation)) + (sha256 + (base32 "0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg")))) + (properties `((upstream-name . "EnsDb.Hsapiens.v79"))) + (build-system r-build-system) + (propagated-inputs (list r-ensembldb)) + (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v79") + (synopsis "Ensembl based annotation package") + (description "This package exposes an annotation database generated from +Ensembl.") + (license license:artistic2.0))) + (define-public r-hpo-db (package (name "r-hpo-db") @@ -269,13 +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) @@ -296,7 +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) @@ -306,7 +327,7 @@ analysis.") 'annotation)) (sha256 (base32 - "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi")))) + "0fgrpjfrsw837ay9cq3wd6gp6sxvwjc7r9spfs4m89vqs2xb0bfc")))) (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs @@ -321,14 +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)) @@ -370,14 +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 @@ -718,14 +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) @@ -743,13 +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) @@ -762,13 +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) @@ -863,7 +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) @@ -872,7 +893,7 @@ from several related annotation packages.") version 'annotation)) (sha256 (base32 - "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) + "1272n72fvj4agszd9cv8l9h9qr2pzmd0rbvdz83x7x03cdddf9rn")))) (properties `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) @@ -933,13 +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) @@ -955,13 +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) @@ -977,13 +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) @@ -999,13 +1020,13 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.14.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j")))) + "1jn556ql6xknfd34qz4bqh6bgc9rccmz6pk41p7ivlzlslz7bp21")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -1021,13 +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) @@ -1067,18 +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") @@ -1278,13 +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) @@ -1466,13 +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 @@ -1553,12 +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)) @@ -1574,12 +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}") @@ -1590,12 +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) @@ -1609,14 +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)) @@ -1632,14 +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)) @@ -1650,21 +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") @@ -1676,13 +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)) @@ -1716,13 +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 @@ -1745,13 +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)) @@ -1765,13 +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/") @@ -1784,13 +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/") @@ -1807,14 +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)) @@ -1830,14 +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 @@ -1864,18 +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 @@ -1886,13 +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) @@ -1912,13 +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 @@ -1953,14 +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") @@ -1975,13 +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") @@ -1991,17 +2050,36 @@ package.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-jaspar2016 + (package + (name "r-jaspar2016") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "JASPAR2016" version 'experiment)) + (sha256 + (base32 "0dyx29f7jnyqcj85j2yrl8jcphi2kymx2y2mk7ws25xcahl5zzpy")))) + (properties `((upstream-name . "JASPAR2016"))) + (build-system r-build-system) + (home-page "https://jaspar.elixir.no/") + (synopsis "Data package for JASPAR 2016") + (description + "This is a data package for JASPAR 2016. To search this databases, +please use the package TFBSTools.") + (license license:gpl2))) + (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)) @@ -2014,17 +2092,45 @@ gene expression indicate a role for enhancer priming in immune response\", publi in Nature Genetics, January 2018.") (license license:gpl2+))) +(define-public r-methylclockdata + (package + (name "r-methylclockdata") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "methylclockData" version + 'experiment)) + (sha256 + (base32 "0q4hiclws0fg03kwvbdwka024gghl1hbmmfficxfghslll78mc3y")))) + (properties `((upstream-name . "methylclockData"))) + (build-system r-build-system) + (propagated-inputs (list r-experimenthub r-experimenthubdata)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/isglobal-brge/methylclockData") + (synopsis "Data for methylclock package") + (description + "This package contains a collection of 9 datasets, andrews and bakulski +cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, +combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, +guintivano dlpfc and saliva gse48472. The data are used to estimate cell +counts using Extrinsic epigenetic age acceleration (EEAA) method. It also +contains a collection of 12 datasets to use with @code{MethylClock} package to +estimate chronological and gestational DNA methylation with estimators to use +with different methylation clocks.") + (license license:expat))) + (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 @@ -2048,13 +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 @@ -2071,13 +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") @@ -2128,14 +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 @@ -2160,13 +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)) @@ -2181,13 +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) @@ -2210,13 +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 @@ -2234,13 +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 @@ -2256,13 +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") @@ -2282,13 +2388,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.18.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr")))) + (base32 "0kfdzc5arzsrdaps7b3r718yawpv1x7wms5jp90j8cxpn0hz07az")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -2315,14 +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)) @@ -2339,14 +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 @@ -2373,13 +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)) @@ -2392,14 +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)) @@ -3250,19 +3356,18 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.16.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "1z46lpd2zi3b88i27qm48wy4acb2xsjh63zgxhfx2y4bgvr29ni7")))) + "1q0ca3pagqzj12kah79jg4py3ibz7qsdl975r2mxhphqwj76gnh8")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs (list r-ape r-assertthat - r-biomformat r-caret r-covr r-deseq2 @@ -3270,7 +3375,6 @@ these biases and construct statistically consistent estimators.") r-dt r-forcats r-ggplot2 - r-glmnet r-gunifrac r-lattice r-limma @@ -3278,9 +3382,9 @@ these biases and construct statistically consistent estimators.") r-matrix r-multiassayexperiment r-plotly - r-plotroc r-rentrez r-reshape2 + r-rocit r-s4vectors r-scales r-shiny @@ -5437,13 +5541,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-densvis (package (name "r-densvis") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "densvis" version)) (sha256 (base32 - "164pyy5l69qhdgqkxjginapvfjy0rjx4p6m83cijz6jbz6kf6gks")))) + "11a112r2ckzphqj3r3fxvablzwgri0j5lx3ggh1z6pfnv113xxwj")))) (properties `((upstream-name . "densvis"))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -5691,13 +5795,13 @@ in Python.") (define-public r-dss (package (name "r-dss") - (version "2.48.0") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 - "1aslbzwqfp609ym98k6cjjf6r1ns9hxcpx4igfjhqf2v0pazz2q8")))) + "1wjd428kz2w3n4ak13h3i1yknm03fh911jrcy2hkcip4z5cssla0")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) @@ -6122,6 +6226,52 @@ multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment} objects can be used within Nebulosa.") (license license:gpl3))) +;; This is a CRAN package but it requires r-rcy3, a Bioconductor package. +(define-public r-netgsa + (package + (name "r-netgsa") + (version "4.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "netgsa" version)) + (sha256 + (base32 "1m9myxsbvbljr038azxzakpbh20a21qhiy20d0ipvjc5asq3kfla")))) + (properties `((upstream-name . "netgsa"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-corpcor + r-data-table + r-dplyr + r-genefilter + r-glassofast + r-glmnet + r-graph + r-graphite + r-httr + r-igraph + r-magrittr + r-matrix + r-msigdbr + r-org-hs-eg-db + r-quadprog + r-rcpp + r-rcppeigen + r-rcy3 + r-reshape2 + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikehellstern/netgsa") + (synopsis "Network-Based gene set analysis") + (description + "This package lets you carry out network-based gene set analysis by +incorporating external information about interactions among genes, as well as +novel interactions learned from data. It implements methods described in +Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, +Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, +Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.") + (license license:gpl3+))) + ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package @@ -6613,13 +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) @@ -6749,13 +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) @@ -7061,13 +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 @@ -7413,13 +7563,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.6") + (version "4.0.14") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0vksak7rv0agar0gplpj2fcp3183l3iyvbqjmx64c7dwpzjh3lb5")))) + "1a0icqi1im4vw2r6wjc5ibjsci7yqcdhk8bn8kyvsp1ld1ri538n")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7757,13 +7907,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0y54kdgb77xqni46pgff1by2ska2jaxfcpq6gk86wb2rym37wlxj")))) + "0i4n735xabdhlg7w2yd31lg65s9b6w12fhzij91hbcp0hs40fvw1")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7822,13 +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) @@ -8327,14 +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, @@ -9083,6 +9233,43 @@ It has function interfaces for: @end itemize") (license license:expat))) +(define-public r-modstrings + (package + (name "r-modstrings") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Modstrings" version)) + (sha256 + (base32 "1jjawwkvdx02ss2vw4ah2b8psgxr01z6r1rkr2pnkmrp2ma7ygks")))) + (properties `((upstream-name . "Modstrings"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/Modstrings") + (synopsis "Working with modified nucleotide sequences") + (description + "Representing nucleotide modifications in a nucleotide sequence is +usually done via special characters from a number of sources. This represents +a challenge to work with in R and the Biostrings package. The Modstrings +package implements this functionallity for RNA and DNA sequences containing +modified nucleotides by translating the character internally in order to work +with the infrastructure of the Biostrings package. For this the +@code{ModRNAString} and @code{ModDNAString} classes and derivates and +functions to construct and modify these objects despite the encoding issues +are implemenented. In addition the conversion from sequences to list like +location information (and the reverse operation) is implemented as well.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") @@ -9831,6 +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") @@ -9924,6 +10173,43 @@ library implementing most of the pipeline's features.") (home-page "https://github.com/BIMSBbioinfo/RCAS") (license license:artistic2.0))) +(define-public r-rcy3 + (package + (name "r-rcy3") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RCy3" version)) + (sha256 + (base32 "0qkjprf2p641j3a60av1l87pd6p17za5w6bp9qyah97jmm19za7m")))) + (properties `((upstream-name . "RCy3"))) + (build-system r-build-system) + (propagated-inputs (list r-base64enc + r-base64url + r-biocgenerics + r-fs + r-glue + r-gplots + r-graph + r-httr + r-irdisplay + r-irkernel + r-rcolorbrewer + r-rcurl + r-rjsonio + r-stringi + r-uuid + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/cytoscape/RCy3") + (synopsis "Functions to access and control Cytoscape") + (description + "Vizualize, analyze and explore networks using Cytoscape via R. Anything +you can do using the graphical user interface of Cytoscape, you can now do +with a single RCy3 function.") + (license license:expat))) + (define-public r-regioner (package (name "r-regioner") @@ -10851,6 +11137,49 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-sictools + (package + (name "r-sictools") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SICtools" version)) + (sha256 + (base32 "0bcajjvkaxmr8bdij8xln7a3nmxbm7jkjvg2v6p8kd0xr3q9a70q")))) + (properties `((upstream-name . "SICtools"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-curses + (lambda _ + (substitute* "src/Makefile" + (("^LIBCURSES.*") + "LIBCURSES=-lncurses\n"))))))) + (propagated-inputs (list r-biostrings + r-doparallel + r-genomicranges + r-iranges + r-matrixstats + r-plyr + r-rsamtools + r-stringr)) + (inputs (list ncurses)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/SICtools") + (synopsis + "Find SNV/Indel differences between two bam files with near relationship") + (description + "This package is to find SNV/Indel differences between two @file{bam} +files with near relationship in a way of pairwise comparison through each base +position across the genome region of interest. The difference is inferred by +Fisher test and euclidean distance, the input of which is the base +count (A,T,G,C) in a given position and read counts for indels that span no +less than 2bp on both sides of indel region.") + (license license:gpl2+))) + (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") @@ -11170,6 +11499,73 @@ includes a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.") (license license:gpl3))) +(define-public r-trna + (package + (name "r-trna") + (version "1.20.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tRNA" version)) + (sha256 + (base32 + "0mcpql3zf1gw2k6gfyqycycc8li00818gd9qzs8s3wva7kxbpn89")))) + (properties + `((upstream-name . "tRNA"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-ggplot2 + r-iranges + r-modstrings + r-s4vectors + r-scales + r-stringr + r-structstrings + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tRNA") + (synopsis "Analyzing tRNA sequences and structures") + (description + "The tRNA package allows tRNA sequences and structures to be accessed and +used for subsetting. In addition, it provides visualization tools to compare +feature parameters of multiple tRNA sets and correlate them to additional +data. The tRNA package uses GRanges objects as inputs requiring only few +additional column data sets.") + (license license:gpl3))) + +(define-public r-trnadbimport + (package + (name "r-trnadbimport") + (version "1.20.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tRNAdbImport" version)) + (sha256 + (base32 "1i2mismx914ijys13wwz50gkk682rklp36aci270nc7vx78hynni")))) + (properties `((upstream-name . "tRNAdbImport"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-genomicranges + r-httr2 + r-iranges + r-modstrings + r-s4vectors + r-stringr + r-structstrings + r-trna + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tRNAdbImport") + (synopsis "Importing from tRNAdb and mitotRNAdb as GRanges objects") + (description + "@code{tRNAdbImport} imports the entries of the @code{tRNAdb} and +@code{mtRNAdb} as GRanges object.") + (license license:gpl3))) + (define-public r-scds (package (name "r-scds") @@ -11358,6 +11754,40 @@ associations. Each interaction is associated with a combined confidence score that integrates the various evidences.") (license license:gpl2))) +(define-public r-structstrings + (package + (name "r-structstrings") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Structstrings" version)) + (sha256 + (base32 "10j1khhjd30wn9yfz4jhgx34z0yyijgwgydr8ric52337vwpx6dl")))) + (properties `((upstream-name . "Structstrings"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biostrings + r-crayon + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FelixErnst/Structstrings") + (synopsis "Implementation of the dot bracket annotations with Biostrings") + (description + "The Structstrings package implements the widely used dot bracket +annotation for storing base pairing information in structured +RNA. Structstrings uses the infrastructure provided by the Biostrings package +and derives the @code{DotBracketString} and related classes from the BString +class. From these, base pair tables can be produced for in depth analysis. +In addition, the loop indices of the base pairs can be retrieved as well. For +better efficiency, information conversion is implemented in C, inspired to a +large extend by the @code{ViennaRNA} package.") + (license license:artistic2.0))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") @@ -12422,18 +12852,18 @@ 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 @@ -15187,18 +15617,18 @@ 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") @@ -16089,6 +16519,37 @@ type and symbol colors.") position-specific scores within R and Bioconductor.") (license license:artistic2.0))) +(define-public r-genomicstate + (package + (name "r-genomicstate") + (version "0.99.15") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicState" version + 'annotation)) + (sha256 + (base32 "1r7z3n6wyrd2cclj5b7sg15wpmjdh9k5b1hjlw7jjx8j384l7l1h")))) + (properties `((upstream-name . "GenomicState"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-bumphunter + r-derfinder + r-genomeinfodb + r-genomicfeatures + r-iranges + r-org-hs-eg-db + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/LieberInstitute/GenomicState") + (synopsis "Build and access GenomicState objects") + (description + "This package contains functions for building @code{GenomicState} objects +from different annotation sources such as Gencode. It also provides access to +these files at JHPCE.") + (license license:artistic2.0))) + (define-public r-atacseqqc (package (name "r-atacseqqc") @@ -16783,14 +17244,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "061ihzj8pn2g393q1gdq2jssanxm9gh5qm37fz4gna2hbd6bf79p")))) + "170s260sp880d3rb256189jvfnnmyzf9nxh8bvksng6yp561r8dc")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17592,14 +18053,14 @@ 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)) @@ -17615,6 +18076,78 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flames + (package + (name "r-flames") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FLAMES" version)) + (sha256 + (base32 "0937zag0h4bvpapld267s5gz36h8zgjrgvbng9m7czdd8w6064ns")))) + (properties `((upstream-name . "FLAMES"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-build-system + (lambda _ + ;; One target uses & instead of &&, which leads to a command + ;; being run despite the check failing. + (substitute* "src/Makevars" + ((" & ") " && "))))))) + (propagated-inputs + (list r-bambu + r-basilisk + r-biocgenerics + r-biostrings + r-circlize + r-complexheatmap + r-cowplot + r-dplyr + r-dropletutils + r-future + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-gridextra + r-igraph + r-jsonlite + r-magrittr + r-matrix + r-multiassayexperiment + r-rcolorbrewer + r-rcpp + r-reticulate + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tidyr + r-withr + r-zlibbioc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/OliverVoogd/FLAMES") + (synopsis + "Full Length Analysis of Mutations and Splicing in long read RNA-seq data") + (description + "This is a package for semi-supervised isoform detection and annotation +from both bulk and single-cell long read RNA-seq data. Flames provides +automated pipelines for analysing isoforms, as well as intermediate functions +for manual execution.") + (license license:gpl2+))) + (define-public r-flowai (package (name "r-flowai") @@ -17747,41 +18280,23 @@ datasets, which increases the analytical flexibility and the statistical power of the analyses while minimizing technical noise.") (license license:expat)))) +;; This package bundles a version of Boost. We cannot use the latest version +;; of Boost here, as we also need to make sure that the BH (r-bh) package is +;; compatible with whatever this package bundles. (define-public r-cytolib (package (name "r-cytolib") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1r2slhzrp3gf45k5gknqgj3vjz7p0rx2yjzrbp020inj82fp4mgi")) - ;; Remove bundled boost sources - (modules '((guix build utils))) - (snippet - '(delete-file-recursively "src/boost")))) + "1kagik93ddcl3m1i2bqzzlh18lbxywfn3pxmp47p45kayzxzldrf")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'unbundle - (lambda _ - (substitute* "src/Makevars.in" - (("\\$\\(USERLIB\\): \\$\\{boost_fs_objs\\}") - "$(USERLIB):") - (("\\$\\{cytolib_objs\\} \\$\\{boost_fs_objs\\} \\$\\{boost_sys_objs\\}") - "${cytolib_objs}") - (("PKG_CPPFLAGS =") - "PKG_CPPFLAGS = -lboost_filesystem") - #; - (("^BOOSTFSLIB.*") - (string-append "BOOSTFSLIB=" - #$(this-package-input "boost") "/libboost_filesystem.so\n")))))))) - (inputs (list boost openblas protobuf zlib)) + (inputs (list openblas protobuf zlib)) (native-inputs (list r-knitr)) (propagated-inputs @@ -17796,14 +18311,14 @@ 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 @@ -18012,14 +18527,14 @@ 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 @@ -18059,14 +18574,14 @@ 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 @@ -20003,13 +20518,13 @@ 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) @@ -20021,8 +20536,9 @@ monograph.") r-callr r-codetools r-graph - r-httr + r-httr2 r-knitr + r-rvest r-stringdist)) (native-inputs (list r-knitr)) @@ -20140,6 +20656,34 @@ and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) +(define-public r-experimenthubdata + (package + (name "r-experimenthubdata") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ExperimentHubData" version)) + (sha256 + (base32 "0msg3wpz1ppvwc4dsm9bz9h4y4hz67xr1xwp4vv4100sg0i5v9jn")))) + (properties `((upstream-name . "ExperimentHubData"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationhubdata + r-biocgenerics + r-biocmanager + r-curl + r-dbi + r-experimenthub + r-httr + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ExperimentHubData") + (synopsis "Add resources to ExperimentHub") + (description + "This package provides functions to add metadata to @code{ExperimentHub} +db and resource files to AWS S3 buckets.") + (license license:artistic2.0))) + (define-public r-grohmm (package (name "r-grohmm") @@ -21544,14 +22088,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.30.0") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0vq3216jk389mjnz5kx0i6fwmkypp21rshvv9ldcy327h6vk1ylj")))) + "06b454ydd8n8xbswxf1hacm3g2nr0ik0gg08pr7crgnsm0r3vpvs")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -23029,14 +23573,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.14.1") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1v67z53y2nnss6l6nk7f557kn0d5syg9n0zdgddpsz26rwdmp8ai")))) + "0hmx2jpfmjv87mp99mzbbzg00m6arpkpc5prkfav065iwjqbqnpd")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -24019,14 +24563,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.20.1") + (version "1.20.3") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "00wygiv6k75bx5qs27qlq9l6ajv9gl2bbyqi2gv6jaaaj167q4sd")))) + "0hlx5kvhspc62p68gz53n0scwji3zvfv915fm8rzw3l8h2hjh3y7")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |