diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 2014 |
1 files changed, 1681 insertions, 333 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e584a7bced..863b97463a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) @@ -40,11 +41,34 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) + #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations +(define-public r-reactome-db + (package + (name "r-reactome-db") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "reactome.db" version 'annotation)) + (sha256 + (base32 + "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) + (properties `((upstream-name . "reactome.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/reactome.db/") + (synopsis "Annotation maps for reactome") + (description + "This package provides a set of annotation maps for the REACTOME +database, assembled using data from REACTOME.") + (license license:cc-by4.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -876,19 +900,72 @@ examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) +(define-public r-curatedtcgadata + (package + (name "r-curatedtcgadata") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) + (sha256 + (base32 + "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) + (properties + `((upstream-name . "curatedTCGAData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-experimenthub" ,r-experimenthub) + ("r-hdf5array" ,r-hdf5array) + ("r-multiassayexperiment" ,r-multiassayexperiment) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/curatedTCGAData/") + (synopsis "Curated data from The Cancer Genome Atlas") + (description + "This package provides publicly available data from The Cancer Genome +Atlas (TCGA) as @code{MultiAssayExperiment} objects. +@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy +number, mutation, microRNA, protein, and others) with clinical / pathological +data. It also links assay barcodes with patient identifiers, enabling +harmonized subsetting of rows (features) and columns (patients / samples) +across the entire multi-'omics experiment.") + (license license:artistic2.0))) + ;;; Packages +(define-public r-biocversion + (package + (name "r-biocversion") + (version "3.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocVersion" version)) + (sha256 + (base32 + "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) + (properties `((upstream-name . "BiocVersion"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BiocVersion/") + (synopsis "Set the appropriate version of Bioconductor packages") + (description + "This package provides repository information for the appropriate version +of Bioconductor.") + (license license:artistic2.0))) + (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) + "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -902,14 +979,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) + "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -923,14 +1000,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) + "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -951,14 +1028,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) + "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -976,14 +1053,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.56.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) + "12r9ljkp3xix0xq8d1488c8wb3a4whb805v48ynmv985bs3phc71")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1015,14 +1092,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) + "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1043,14 +1120,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) + "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1070,14 +1147,14 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) + "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") @@ -1088,14 +1165,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.5") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) + "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1117,14 +1194,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) + "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -1165,14 +1242,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) + "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -1190,14 +1267,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) + "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -1225,14 +1302,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) + "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1259,14 +1336,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) + "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -1288,14 +1365,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) + "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -1333,14 +1410,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) + "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs @@ -1366,14 +1443,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) + "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -1404,13 +1481,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) + "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -1451,14 +1528,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.2") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) + "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1507,12 +1584,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) + (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -1526,12 +1603,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) + (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -1546,12 +1623,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) + (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -1569,20 +1646,21 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) + (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) @@ -1601,14 +1679,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) + "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -1627,14 +1705,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) + "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -1661,14 +1739,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) + "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -1700,14 +1778,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) + "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -1728,14 +1806,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) + "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -1760,14 +1838,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) + "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -1799,14 +1877,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) + "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -1819,14 +1897,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) + "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1845,14 +1923,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) + "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -1872,14 +1950,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) + "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -1896,14 +1974,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) + "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1921,14 +1999,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.14.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) + "03cf9c94ra4f847ndlf8sn2cq1kl1055514wjq0lqbvlbfdj1dq3")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -1937,12 +2015,14 @@ genes or proteins in these datasets.") ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-desolve" ,r-desolve) + ("r-gdata" ,r-gdata) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) ("r-plgem" ,r-plgem) - ("r-preprocesscore" ,r-preprocesscore) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) @@ -1963,14 +2043,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) + "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -1990,14 +2070,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) + "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -2016,19 +2096,19 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.2.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) + "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) + `(("r-biocparallel" ,r-biocparallel) + ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) @@ -2047,14 +2127,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) + "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -2079,29 +2159,37 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "2.14.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) + "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-ggplot-multistats" ,r-ggplot-multistats) ("r-ggplot2" ,r-ggplot2) ("r-ggthemes" ,r-ggthemes) - ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) + ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) + ("r-rcpphnsw" ,r-rcpphnsw) + ("r-rspectra" ,r-rspectra) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) + ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) ("r-vim" ,r-vim))) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") @@ -2113,14 +2201,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) + "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -2139,14 +2227,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) + "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -2177,13 +2265,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) + "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -2200,14 +2288,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) + "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2251,14 +2339,14 @@ clusters).") (define-public r-deds (package (name "r-deds") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEDS" version)) (sha256 (base32 - "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) + "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) (properties `((upstream-name . "DEDS"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DEDS/") @@ -2300,14 +2388,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) + "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -2324,14 +2412,14 @@ gene and isoform level using RNA-seq data") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) + "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran) @@ -2354,14 +2442,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) + "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -2384,14 +2472,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) + "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -2418,19 +2506,18 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) + "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-blme" ,r-blme) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) @@ -2452,14 +2539,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) + "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2569,14 +2656,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) + "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -2596,14 +2683,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) + "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -2632,14 +2719,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) + "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -2672,14 +2759,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.52.0") + (version "2.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) + "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -2703,14 +2790,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) + "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -2724,14 +2811,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) + "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2750,14 +2837,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) + "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2784,14 +2871,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) + "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -2833,14 +2920,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) + "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -2877,14 +2964,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) + "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -2916,14 +3003,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) + "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -2975,14 +3062,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) + "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -3104,14 +3191,14 @@ published results; and a routine for graphical display.") (define-public r-triform (package (name "r-triform") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 - "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) + "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -3128,14 +3215,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) + "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -3168,14 +3255,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) + "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -3193,14 +3280,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) + "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -3220,14 +3307,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) + "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -3251,14 +3338,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) + "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -3273,14 +3360,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) + "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3303,14 +3390,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.10.2") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) + "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -3337,14 +3424,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.4.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) + "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3360,8 +3447,7 @@ data.") ("r-igraph" ,r-igraph) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-upsetr" ,r-upsetr))) + ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -3373,14 +3459,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.12.0") + (version "3.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) + "1y1l3yf1r1ykl9ngipvyzl5hbxxsfz7z5q5rcywkyss2b2b6gsg8")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -3406,14 +3492,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh")))) + "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3447,14 +3533,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) + "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) (build-system r-build-system) (arguments `(#:phases @@ -3483,14 +3569,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) + "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -3506,14 +3592,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) + "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -3534,14 +3620,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) + "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -3556,14 +3642,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) + "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -3579,14 +3665,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) + "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -3611,14 +3697,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) + "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -3636,14 +3722,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) + "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -3682,14 +3768,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) + "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -3707,19 +3793,20 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.32.0") + (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) + "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-seqlogo" ,r-seqlogo))) (home-page "https://bioconductor.org/packages/rGADEM/") @@ -3732,14 +3819,14 @@ genomic sequence data.") (define-public r-motiv (package (name "r-motiv") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 - "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) + "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs @@ -3747,6 +3834,7 @@ genomic sequence data.") (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-rgadem" ,r-rgadem) @@ -3763,19 +3851,20 @@ distributions, modules and filter motifs.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) + "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-biostrings" ,r-biostrings) + ("r-ggplot2" ,r-ggplot2) ("r-grimport2" ,r-grimport2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-motiv" ,r-motiv) @@ -3794,14 +3883,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) + "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -3825,14 +3914,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.5") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) + "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -3870,14 +3959,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) + "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -3917,14 +4006,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) + "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -3947,14 +4036,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) + "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) @@ -3972,14 +4061,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) + "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -3997,14 +4086,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) + "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -4038,21 +4127,23 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) + "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) + ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/AUCell/") @@ -4073,14 +4164,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.26.0") + (version "4.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) + "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -4112,14 +4203,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) + "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4144,14 +4235,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) + "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -4171,14 +4262,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) + "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -4208,14 +4299,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) + "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -4248,14 +4339,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) + "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4284,14 +4375,14 @@ gene-specific bidning is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) + "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4312,14 +4403,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) + "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) @@ -4334,14 +4425,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) + "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4365,14 +4456,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) + "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4400,14 +4491,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) + "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4429,14 +4520,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) + "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs @@ -4466,14 +4557,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) + "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -4490,19 +4581,20 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.6.2") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v")))) + "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) @@ -4526,14 +4618,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) + "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -4550,14 +4642,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) + "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4582,14 +4674,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) + "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -4603,14 +4695,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) + "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -4636,14 +4728,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) + "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -4663,14 +4755,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) + "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs @@ -4686,14 +4778,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) + "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://github.com/saezlab/progeny") @@ -4708,14 +4800,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) + "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -4731,14 +4823,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.8.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) + "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -4761,14 +4853,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) + "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4791,14 +4883,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) + "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs @@ -4814,14 +4906,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) + "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -4855,18 +4947,28 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) + "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) - (native-inputs - `(("which" ,which))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + (substitute* "src/Makefile" + (("`hostname`") "guix") + (("`date`") "0") + ;; Avoid shelling out to "which". + (("^CC =.*") (which "gcc")) + (("^CPP =.*") (which "g++"))) + #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) @@ -4883,14 +4985,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) + "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs @@ -4928,14 +5030,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) + "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -4969,14 +5071,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) + "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -4998,14 +5100,14 @@ routines to analyse the resulting networks and their natural projections.") (define-public r-birta (package (name "r-birta") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 - "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) + "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5024,19 +5126,56 @@ conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) +(define-public r-multidataset + (package + (name "r-multidataset") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiDataSet" version)) + (sha256 + (base32 + "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) + (properties `((upstream-name . "MultiDataSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-qqman" ,r-qqman) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/MultiDataSet/") + (synopsis "Implementation of MultiDataSet and ResultSet") + (description + "This package provides an implementation of the BRGE's (Bioinformatic +Research Group in Epidemiology from Center for Research in Environmental +Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for +integrating multi omics data sets and ResultSet is a container for omics +results. This package contains base classes for MEAL and rexposome +packages.") + (license license:expat))) + (define-public r-ropls (package (name "r-ropls") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) + "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp")))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") @@ -5063,18 +5202,19 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) + "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) + ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs @@ -5098,14 +5238,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) + "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5137,14 +5277,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.7") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) + "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5161,14 +5301,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -5187,14 +5327,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -5209,29 +5349,46 @@ and to both short and long sequence reads.") cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) + (properties `((upstream-name . "cytolib"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/cytolib/") + (synopsis "C++ infrastructure for working with gated cytometry") + (description + "This package provides the core data structure and API to represent and +interact with gated cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") - (version "1.50.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-corpcor" ,r-corpcor) - ("r-graph" ,r-graph) - ("r-mass" ,r-mass) + ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) + ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -5242,14 +5399,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -5265,25 +5422,361 @@ Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) +(define-public r-ncdfflow + (package + (name "r-ncdfflow") + (version "2.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ncdfFlow" version)) + (sha256 + (base32 + "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) + (properties `((upstream-name . "ncdfFlow"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-flowcore" ,r-flowcore) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ncdfFlow/") + (synopsis "HDF5 based storage for flow cytometry data") + (description + "This package provides HDF5 storage based methods and functions for +manipulation of flow cytometry data.") + (license license:artistic2.0))) + +(define-public r-ggcyto + (package + (name "r-ggcyto") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggcyto" version)) + (sha256 + (base32 + "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8")))) + (properties `((upstream-name . "ggcyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/RGLab/ggcyto/issues") + (synopsis "Visualize Cytometry data with ggplot") + (description + "With the dedicated fortify method implemented for @code{flowSet}, +@code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow +cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper +and some custom layers also make it easy to add gates and population +statistics to the plot.") + (license license:artistic2.0))) + +(define-public r-flowviz + (package + (name "r-flowviz") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowViz" version)) + (sha256 + (base32 + "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) + (properties `((upstream-name . "flowViz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-flowcore" ,r-flowcore) + ("r-hexbin" ,r-hexbin) + ("r-idpmisc" ,r-idpmisc) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/flowViz/") + (synopsis "Visualization for flow cytometry") + (description + "This package provides visualization tools for flow cytometry data.") + (license license:artistic2.0))) + +(define-public r-flowclust + (package + (name "r-flowclust") + (version "3.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowClust" version)) + (sha256 + (base32 + "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) + (properties `((upstream-name . "flowClust"))) + (build-system r-build-system) + (arguments + `(#:configure-flags + (list "--configure-args=--enable-bundled-gsl=no"))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-corpcor" ,r-corpcor) + ("r-ellipse" ,r-ellipse) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-mnormt" ,r-mnormt))) + (inputs + `(("gsl" ,gsl))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://bioconductor.org/packages/flowClust") + (synopsis "Clustering for flow cytometry") + (description + "This package provides robust model-based clustering using a t-mixture +model with Box-Cox transformation.") + (license license:artistic2.0))) + +;; TODO: this package bundles an old version of protobuf. It's not easy to +;; make it use our protobuf package instead. +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) + (properties `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-bundled-sources + (lambda _ + (with-directory-excursion "src" + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + #t))))) + (home-page "https://bioconductor.org/packages/RProtoBufLib/") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description + "This package provides the headers and static library of Protocol buffers +for other R packages to compile and link against.") + (license license:bsd-3))) + +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762")))) + (properties `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/flowWorkspace/") + (synopsis "Infrastructure for working with cytometry data") + (description + "This package is designed to facilitate comparison of automated gating +methods against manual gating done in flowJo. This package allows you to +import basic flowJo workspaces into BioConductor and replicate the gating from +flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of +samples, compensation, and transformation are performed so that the output +matches the flowJo analysis.") + (license license:artistic2.0))) + +(define-public r-flowstats + (package + (name "r-flowstats") + (version "3.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowStats" version)) + (sha256 + (base32 + "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) + (properties `((upstream-name . "flowStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-fda" ,r-fda) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-kernsmooth" ,r-kernsmooth) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rrcov" ,r-rrcov))) + (home-page "http://www.github.com/RGLab/flowStats") + (synopsis "Statistical methods for the analysis of flow cytometry data") + (description + "This package provides methods and functionality to analyze flow data +that is beyond the basic infrastructure provided by the @code{flowCore} +package.") + (license license:artistic2.0))) + +(define-public r-opencyto + (package + (name "r-opencyto") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "openCyto" version)) + (sha256 + (base32 + "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) + (properties `((upstream-name . "openCyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-data-table" ,r-data-table) + ("r-flowclust" ,r-flowclust) + ("r-flowcore" ,r-flowcore) + ("r-flowstats" ,r-flowstats) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-graph" ,r-graph) + ("r-gtools" ,r-gtools) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-r-utils" ,r-r-utils) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page "https://bioconductor.org/packages/openCyto") + (synopsis "Hierarchical gating pipeline for flow cytometry data") + (description + "This package is designed to facilitate the automated gating methods in a +sequential way to mimic the manual gating strategy.") + (license license:artistic2.0))) + +(define-public r-cytoml + (package + (name "r-cytoml") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CytoML" version)) + (sha256 + (base32 + "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1")))) + (properties `((upstream-name . "CytoML"))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggcyto" ,r-ggcyto) + ("r-graph" ,r-graph) + ("r-jsonlite" ,r-jsonlite) + ("r-lattice" ,r-lattice) + ("r-ncdfflow" ,r-ncdfflow) + ("r-opencyto" ,r-opencyto) + ("r-plyr" ,r-plyr) + ("r-rbgl" ,r-rbgl) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/RGLab/CytoML") + (synopsis "GatingML interface for cross platform cytometry data sharing") + (description + "This package provides an interface to implementations of the GatingML2.0 +standard to exchange gated cytometry data with other software platforms.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) + ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) - ("r-flowutils" ,r-flowutils) + ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") @@ -5296,14 +5789,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.5") + (version "6.10.6") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) + "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -5338,29 +5831,21 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-syntax-error - (lambda _ - (substitute* "src/Makevars" - ((" & ") " && ")) - #t))))) (propagated-inputs `(("r-beanplot" ,r-beanplot) - ("r-biocparallel" ,r-biocparallel) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gplots" ,r-gplots) @@ -5371,6 +5856,7 @@ delete entire rows with missing data.") ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) + ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") @@ -5388,14 +5874,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) + "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -5423,14 +5909,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) + "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5530,14 +6016,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) + "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) @@ -5551,16 +6037,18 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) + "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -5597,14 +6085,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) + "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -5634,14 +6122,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) + "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -5691,14 +6179,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) + "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -5719,14 +6207,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw")))) + "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -5747,14 +6235,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a")))) + "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -5772,14 +6260,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) + "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -5818,14 +6306,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) + "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -5857,14 +6345,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) + "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -5904,14 +6392,14 @@ populations, splice site strength, conservation, etc.") (define-public r-genomegraphs (package (name "r-genomegraphs") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeGraphs" version)) (sha256 (base32 - "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd")))) + "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs @@ -5932,14 +6420,14 @@ same genome coordinate system.") (define-public r-wavetiling (package (name "r-wavetiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 - "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) + "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs @@ -5963,14 +6451,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd")))) + "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -6005,14 +6493,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) + "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -6038,14 +6526,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a")))) + "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -6059,3 +6547,863 @@ features (e.g. genes, microRNAs).") data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activedriverwgs + (package + (name "r-activedriverwgs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriverWGS" version)) + (sha256 + (base32 + "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) + (properties + `((upstream-name . "ActiveDriverWGS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-plyr" ,r-plyr) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") + (synopsis "Driver discovery tool for cancer whole genomes") + (description + "This package provides a method for finding an enrichment of cancer +simple somatic mutations (SNVs and Indels) in functional elements across the +human genome. ActiveDriverWGS detects coding and noncoding driver elements +using whole genome sequencing data.") + (license license:gpl3))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activepathways + (package + (name "r-activepathways") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivePathways" version)) + (sha256 + (base32 + "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) + (properties + `((upstream-name . "ActivePathways"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-metap" ,r-metap))) + (home-page "https://cran.r-project.org/web/packages/ActivePathways/") + (synopsis "Multivariate pathway enrichment analysis") + (description + "This package represents an integrative method of analyzing multi omics +data that conducts enrichment analysis of annotated gene sets. ActivePathways +uses a statistical data fusion approach, rationalizes contributing evidence +and highlights associated genes, improving systems-level understanding of +cellular organization in health and disease.") + (license license:gpl3))) + +(define-public r-bgmix + (package + (name "r-bgmix") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BGmix" version)) + (sha256 + (base32 + "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) + (properties `((upstream-name . "BGmix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth))) + (home-page "https://bioconductor.org/packages/BGmix/") + (synopsis "Bayesian models for differential gene expression") + (description + "This package provides fully Bayesian mixture models for differential +gene expression.") + (license license:gpl2))) + +(define-public r-bgx + (package + (name "r-bgx") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bgx" version)) + (sha256 + (base32 + "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) + (properties `((upstream-name . "bgx"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-gcrma" ,r-gcrma) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/bgx/") + (synopsis "Bayesian gene expression") + (description + "This package provides tools for Bayesian integrated analysis of +Affymetrix GeneChips.") + (license license:gpl2))) + +(define-public r-bhc + (package + (name "r-bhc") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BHC" version)) + (sha256 + (base32 + "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) + (properties `((upstream-name . "BHC"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BHC/") + (synopsis "Bayesian hierarchical clustering") + (description + "The method implemented in this package performs bottom-up hierarchical +clustering, using a Dirichlet Process (infinite mixture) to model uncertainty +in the data and Bayesian model selection to decide at each step which clusters +to merge. This avoids several limitations of traditional methods, for example +how many clusters there should be and how to choose a principled distance +metric. This implementation accepts multinomial (i.e. discrete, with 2+ +categories) or time-series data. This version also includes a randomised +algorithm which is more efficient for larger data sets.") + (license license:gpl3))) + +(define-public r-bicare + (package + (name "r-bicare") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BicARE" version)) + (sha256 + (base32 + "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) + (properties `((upstream-name . "BicARE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-gseabase" ,r-gseabase) + ("r-multtest" ,r-multtest))) + (home-page "http://bioinfo.curie.fr") + (synopsis "Biclustering analysis and results exploration") + (description + "This is a package for biclustering analysis and exploration of +results.") + (license license:gpl2))) + +(define-public r-bifet + (package + (name "r-bifet") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiFET" version)) + (sha256 + (base32 + "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) + (properties `((upstream-name . "BiFET"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-poibin" ,r-poibin))) + (home-page "https://bioconductor.org/packages/BiFET") + (synopsis "Bias-free footprint enrichment test") + (description + "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are +over-represented in target regions compared to background regions after +correcting for the bias arising from the imbalance in read counts and GC +contents between the target and background regions. For a given TF k, BiFET +tests the null hypothesis that the target regions have the same probability of +having footprints for the TF k as the background regions while correcting for +the read count and GC content bias.") + (license license:gpl3))) + +(define-public r-rsbml + (package + (name "r-rsbml") + (version "2.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rsbml" version)) + (sha256 + (base32 + "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) + (properties `((upstream-name . "rsbml"))) + (build-system r-build-system) + (inputs + `(("libsbml" ,libsbml) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-graph" ,r-graph))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://www.sbml.org") + (synopsis "R support for SBML") + (description + "This package provides an R interface to libsbml for SBML parsing, +validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") + (license license:artistic2.0))) + +(define-public r-hypergraph + (package + (name "r-hypergraph") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hypergraph" version)) + (sha256 + (base32 + "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) + (properties `((upstream-name . "hypergraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-graph" ,r-graph))) + (home-page "https://bioconductor.org/packages/hypergraph") + (synopsis "Hypergraph data structures") + (description + "This package implements some simple capabilities for representing and +manipulating hypergraphs.") + (license license:artistic2.0))) + +(define-public r-hyperdraw + (package + (name "r-hyperdraw") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hyperdraw" version)) + (sha256 + (base32 + "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) + (properties `((upstream-name . "hyperdraw"))) + (build-system r-build-system) + (inputs `(("graphviz" ,graphviz))) + (propagated-inputs + `(("r-graph" ,r-graph) + ("r-hypergraph" ,r-hypergraph) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/hyperdraw") + (synopsis "Visualizing hypergraphs") + (description + "This package provides functions for visualizing hypergraphs.") + (license license:gpl2+))) + +(define-public r-biggr + (package + (name "r-biggr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiGGR" version)) + (sha256 + (base32 + "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) + (properties `((upstream-name . "BiGGR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hyperdraw" ,r-hyperdraw) + ("r-hypergraph" ,r-hypergraph) + ("r-lim" ,r-lim) + ("r-limsolve" ,r-limsolve) + ("r-rsbml" ,r-rsbml) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/BiGGR/") + (synopsis "Constraint based modeling using metabolic reconstruction databases") + (description + "This package provides an interface to simulate metabolic reconstruction +from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic +reconstruction databases. The package facilitates @dfn{flux balance +analysis} (FBA) and the sampling of feasible flux distributions. Metabolic +networks and estimated fluxes can be visualized with hypergraphs.") + (license license:gpl3+))) + +(define-public r-bigmemoryextras + (package + (name "r-bigmemoryextras") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigmemoryExtras" version)) + (sha256 + (base32 + "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) + (properties + `((upstream-name . "bigmemoryExtras"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory))) + (home-page "https://github.com/phaverty/bigmemoryExtras") + (synopsis "Extension of the bigmemory package") + (description + "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds +safety and convenience features to the @code{filebacked.big.matrix} class from +the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by +monitoring and gracefully restoring the connection to on-disk data and it also +protects against accidental data modification with a filesystem-based +permissions system. Utilities are provided for using @code{BigMatrix}-derived +classes as @code{assayData} matrices within the @code{Biobase} package's +@code{eSet} family of classes. @code{BigMatrix} provides some optimizations +related to attaching to, and indexing into, file-backed matrices with +dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, +a file-backed matrix with factor properties.") + (license license:artistic2.0))) + +(define-public r-bigpint + (package + (name "r-bigpint") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigPint" version)) + (sha256 + (base32 + "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk")))) + (properties `((upstream-name . "bigPint"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-hexbin" ,r-hexbin) + ("r-hmisc" ,r-hmisc) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape" ,r-reshape) + ("r-shiny" ,r-shiny) + ("r-shinycssloaders" ,r-shinycssloaders) + ("r-shinydashboard" ,r-shinydashboard) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/lindsayrutter/bigPint") + (synopsis "Big multivariate data plotted interactively") + (description + "This package provides methods for visualizing large multivariate +datasets using static and interactive scatterplot matrices, parallel +coordinate plots, volcano plots, and litre plots. It includes examples for +visualizing RNA-sequencing datasets and differentially expressed genes.") + (license license:gpl3))) + +(define-public r-chemminer + (package + (name "r-chemminer") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChemmineR" version)) + (sha256 + (base32 + "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) + (properties `((upstream-name . "ChemmineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson) + ("r-rsvg" ,r-rsvg))) + (home-page "https://github.com/girke-lab/ChemmineR") + (synopsis "Cheminformatics toolkit for R") + (description + "ChemmineR is a cheminformatics package for analyzing drug-like small +molecule data in R. It contains functions for efficient processing of large +numbers of molecules, physicochemical/structural property predictions, +structural similarity searching, classification and clustering of compound +libraries with a wide spectrum of algorithms. In addition, it offers +visualization functions for compound clustering results and chemical +structures.") + (license license:artistic2.0))) + +(define-public r-bioassayr + (package + (name "r-bioassayr") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bioassayR" version)) + (sha256 + (base32 + "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) + (properties `((upstream-name . "bioassayR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-chemminer" ,r-chemminer) + ("r-dbi" ,r-dbi) + ("r-matrix" ,r-matrix) + ("r-rjson" ,r-rjson) + ("r-rsqlite" ,r-rsqlite) + ("r-xml" ,r-xml))) + (home-page "https://github.com/TylerBackman/bioassayR") + (synopsis "Cross-target analysis of small molecule bioactivity") + (description + "bioassayR is a computational tool that enables simultaneous analysis of +thousands of bioassay experiments performed over a diverse set of compounds +and biological targets. Unique features include support for large-scale +cross-target analyses of both public and custom bioassays, generation of +@dfn{high throughput screening fingerprints} (HTSFPs), and an optional +preloaded database that provides access to a substantial portion of publicly +available bioactivity data.") + (license license:artistic2.0))) + +(define-public r-biobroom + (package + (name "r-biobroom") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biobroom" version)) + (sha256 + (base32 + "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) + (properties `((upstream-name . "biobroom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/StoreyLab/biobroom") + (synopsis "Turn Bioconductor objects into tidy data frames") + (description + "This package contains methods for converting standard objects +constructed by bioinformatics packages, especially those in Bioconductor, and +converting them to @code{tidy} data. It thus serves as a complement to the +@code{broom} package, and follows the same tidy, augment, glance division of +tidying methods. Tidying data makes it easy to recombine, reshape and +visualize bioinformatics analyses.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + +(define-public r-graphite + (package + (name "r-graphite") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "graphite" version)) + (sha256 + (base32 + "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) + (properties `((upstream-name . 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The client creates +and manages a local cache of files retrieved enabling quick and reproducible +access.") + (license license:artistic2.0))) + +(define-public r-multiassayexperiment + (package + (name "r-multiassayexperiment") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiAssayExperiment" version)) + (sha256 + (base32 + "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc")))) + (properties + `((upstream-name . 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It provides a familiar +Bioconductor user experience by extending concepts from +@code{SummarizedExperiment}, supporting an open-ended mix of standard data +classes for individual assays, and allowing subsetting by genomic ranges or +rownames.") + (license license:artistic2.0))) + +(define-public r-bioconcotk + (package + (name "r-bioconcotk") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocOncoTK" version)) + (sha256 + (base32 + "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) + (properties `((upstream-name . 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The goal is to expose metadata for data mining and +value-added functionality such as package searching, text mining, and +analytics on packages.") + (license license:expat))) + +(define-public r-biocset + (package + (name "r-biocset") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocSet" version)) + (sha256 + (base32 + "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) + (properties `((upstream-name . 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Mapping functionality and +accessing web references for elements/sets are also available in BiocSet.") + (license license:artistic2.0))) + +(define-public r-biocworkflowtools + (package + (name "r-biocworkflowtools") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocWorkflowTools" version)) + (sha256 + (base32 + "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad")))) + (properties + `((upstream-name . 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