diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 1109 |
1 files changed, 680 insertions, 429 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4be8aee15..a8ed2707ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -745,13 +745,13 @@ annotations.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil")))) + "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1072,13 +1072,13 @@ package @code{affy}.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf")))) + "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -1099,13 +1099,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk")))) + "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1165,14 +1165,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.10.1") + (version "3.11.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) + "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1185,13 +1185,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) + "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1205,14 +1205,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) + "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -1226,14 +1226,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) + "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -1254,14 +1254,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) + "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -1279,14 +1279,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.58.4") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw")))) + "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1309,6 +1309,8 @@ problems in CEL-level data to help evaluate performance of quality metrics.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xtable" ,r-xtable))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -1319,14 +1321,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) + "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1347,14 +1349,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) + "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1374,15 +1376,17 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) + "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -1392,14 +1396,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9")))) + "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1411,6 +1415,8 @@ the Human Protein Atlas project.") ("r-memoise" ,r-memoise) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -1421,14 +1427,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) + "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -1452,6 +1458,8 @@ region sets and other genomic features.") ("r-pfam-db" ,r-pfam-db) ("r-r-utils" ,r-r-utils) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -1469,14 +1477,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) + "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -1494,14 +1502,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) + "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -1529,14 +1537,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) + "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1552,6 +1560,8 @@ packages.") ("r-preprocesscore" ,r-preprocesscore) ("r-rsqlite" ,r-rsqlite) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -1563,18 +1573,20 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) + "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://github.com/jdstorey/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -1592,14 +1604,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) + "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -1670,14 +1682,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) + "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -1708,13 +1720,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) + "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -1779,14 +1791,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.20.1") + (version "3.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc")))) + "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1819,6 +1831,8 @@ determining dependencies between variables, code improvement suggestions.") ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -1835,12 +1849,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) + (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -1854,12 +1868,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) + (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -1874,12 +1888,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) + (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -1897,12 +1911,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) + (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -1930,14 +1944,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) + "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -1956,14 +1970,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) + "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -1990,14 +2004,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) + "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -2017,6 +2031,8 @@ datasets.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-sqldf" ,r-sqldf))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -2029,14 +2045,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) + "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -2057,14 +2073,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) + "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -2077,6 +2093,8 @@ parsing of genetic sequencing data from ribosome profiling experiments.") ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -2089,14 +2107,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.20.3") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g")))) + "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -2130,14 +2148,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) + "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -2150,14 +2168,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) + "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2176,20 +2194,22 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) + "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) ("r-jsonlite" ,r-jsonlite) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -2203,14 +2223,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) + "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -2227,14 +2247,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) + "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2252,14 +2272,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.16.3") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp")))) + "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -2279,11 +2299,14 @@ genes or proteins in these datasets.") ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-txdb-mmusculus-ucsc-mm9-knowngene" ,r-txdb-mmusculus-ucsc-mm9-knowngene))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -2296,20 +2319,22 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) + "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -2323,14 +2348,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) + "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -2338,6 +2363,8 @@ demultiplexed, i.e. assigned to their original reference barcode.") ("r-edaseq" ,r-edaseq) ("r-edger" ,r-edger) ("r-mass" ,r-mass))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -2349,14 +2376,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6")))) + "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -2366,6 +2393,8 @@ samples.") ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -2380,14 +2409,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407")))) + "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -2400,6 +2429,8 @@ achieved for all methods using the BiocParallel framework.") ("r-rcpp" ,r-rcpp) ("r-rsvd" ,r-rsvd) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -2412,14 +2443,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.0.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi")))) + "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2430,6 +2461,7 @@ possible, parallelization is achieved using the BiocParallel framework.") ("r-irlba" ,r-irlba) ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) + ("r-nbconvertr" ,r-nbconvertr) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) @@ -2456,14 +2488,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) + "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -2482,14 +2514,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) + "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -2510,6 +2542,8 @@ Viewer (SAV) files, access data, and generate QC plots.") ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -2520,13 +2554,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) + "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -2543,14 +2577,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) + "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2643,14 +2677,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) + "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -2667,29 +2701,32 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v")))) + "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs")))) (build-system r-build-system) (propagated-inputs - `(("r-regioner" ,r-regioner) + `(("r-annotationdbi" ,r-annotationdbi) + ("r-bamsignals" ,r-bamsignals) + ("r-bezier" ,r-bezier) + ("r-biovizbase" ,r-biovizbase) + ("r-digest" ,r-digest) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) ("r-memoise" ,r-memoise) + ("r-regioner" ,r-regioner) + ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb) ("r-s4vectors" ,r-s4vectors) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-bezier" ,r-bezier) - ("r-bamsignals" ,r-bamsignals) - ("r-annotationdbi" ,r-annotationdbi) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -2702,20 +2739,20 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) + "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4")))) (build-system r-build-system) (inputs - `(("gfortran" ,gfortran) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -2732,14 +2769,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) + "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -2747,6 +2784,8 @@ to install interface to SYMPHONY.") ("r-fdrtool" ,r-fdrtool) ("r-lpsymphony" ,r-lpsymphony) ("r-slam" ,r-slam))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -2762,14 +2801,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) + "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -2784,6 +2823,8 @@ independent of the p-value under the null hypothesis.") ("r-shinybs" ,r-shinybs) ("r-shinydashboard" ,r-shinydashboard) ("r-upsetr" ,r-upsetr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -2796,14 +2837,14 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) + "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -2831,14 +2872,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) + "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2871,6 +2912,8 @@ single cell assay data.") ("r-tibble" ,r-tibble) ("r-vgam" ,r-vgam) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -2948,14 +2991,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) + "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -2975,14 +3018,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) + "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -2997,6 +3040,8 @@ assumptions.") ("r-scran" ,r-scran) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -3011,14 +3056,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) + "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -3040,6 +3085,8 @@ distributions.") ("r-rhdf5" ,r-rhdf5) ("r-ruvseq" ,r-ruvseq) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -3051,14 +3098,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.54.1") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) + "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -3070,6 +3117,8 @@ high-throughput analyses.") ("r-readr" ,r-readr) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -3082,14 +3131,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) + "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -3103,14 +3152,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) + "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -3129,14 +3178,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) + "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3163,14 +3212,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) + "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -3202,6 +3251,8 @@ studies.") ("r-s4vectors" ,r-s4vectors) ("r-siggenes" ,r-siggenes) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -3212,14 +3263,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) + "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -3240,6 +3291,8 @@ methylation arrays.") ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -3256,14 +3309,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) + "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -3295,14 +3348,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) + "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -3324,6 +3377,8 @@ especially Illumina Infinium methylation microarrays.") ("r-statmod" ,r-statmod) ("r-vegan" ,r-vegan) ("r-zoo" ,r-zoo))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -3354,14 +3409,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) + "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -3378,6 +3433,8 @@ evaluation of DEG analysis methods.") ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -3476,14 +3533,14 @@ published results; and a routine for graphical display.") (define-public r-triform (package (name "r-triform") - (version "1.28.0") + (version "1.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 - "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) + "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -3500,14 +3557,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh")))) + "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -3540,14 +3597,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1")))) + "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -3565,14 +3622,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05")))) + "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -3594,14 +3651,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) + "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -3625,14 +3682,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) + "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -3647,14 +3704,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) + "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3665,6 +3722,8 @@ phenotype of interest.") ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -3677,14 +3736,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) + "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -3695,8 +3754,7 @@ to multiple hypothesis correction.") ("r-ggplot2" ,r-ggplot2) ("r-gosemsim" ,r-gosemsim) ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors))) + ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/DOSE/") @@ -3713,14 +3771,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.6.1") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x")))) + "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3734,9 +3792,13 @@ data.") ("r-gosemsim" ,r-gosemsim) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) + ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2))) + ("r-reshape2" ,r-reshape2) + ("r-scatterpie" ,r-scatterpie))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -3748,22 +3810,23 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.14.3") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg")))) + "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dose" ,r-dose) + ("r-downloader" ,r-downloader) + ("r-dplyr" ,r-dplyr) ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) ("r-go-db" ,r-go-db) ("r-gosemsim" ,r-gosemsim) ("r-magrittr" ,r-magrittr) @@ -3771,6 +3834,8 @@ All the visualization methods are developed based on ggplot2 graphics.") ("r-qvalue" ,r-qvalue) ("r-rvcheck" ,r-rvcheck) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -3781,14 +3846,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.5") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5")))) + "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3806,6 +3871,7 @@ profiles (GO and KEGG) of gene and gene clusters.") ("r-mlbench" ,r-mlbench) ("r-pls" ,r-pls) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) ("r-rpart" ,r-rpart) ("r-sfsmisc" ,r-sfsmisc) ("r-shiny" ,r-shiny) @@ -3821,14 +3887,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) + "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4")))) (build-system r-build-system) (arguments `(#:phases @@ -3857,14 +3923,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) + "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -3880,14 +3946,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) + "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -3908,14 +3974,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) + "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -3930,14 +3996,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) + "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -3953,14 +4019,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83")))) + "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -3985,14 +4051,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) + "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -4010,14 +4076,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) + "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -4041,6 +4107,8 @@ Affymetrix arrays.") ("r-stringr" ,r-stringr) ("r-vegan" ,r-vegan) ("r-venndiagram" ,r-venndiagram))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -4056,14 +4124,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) + "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -4083,14 +4151,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.34.1") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h")))) + "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -4109,14 +4177,14 @@ genomic sequence data.") (define-public r-motiv (package (name "r-motiv") - (version "1.42.0") + (version "1.43.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 - "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) + "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs @@ -4141,21 +4209,24 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc")))) + (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-splitstackshape" ,r-splitstackshape))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -4165,32 +4236,35 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n")))) + (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-grimport" ,r-grimport) - ("r-stringr" ,r-stringr) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-rtracklayer" ,r-rtracklayer) - ("r-variantannotation" ,r-variantannotation) - ("r-biocparallel" ,r-biocparallel) - ("r-motifstack" ,r-motifstack) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-grimport" ,r-grimport) ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) + ("r-motifdb" ,r-motifdb) + ("r-motifstack" ,r-motifstack) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tfmpvalue" ,r-tfmpvalue) - ("r-motifdb" ,r-motifdb))) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -4213,14 +4287,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) + "008f2mjcyyiz84ilrsldpqwvxy2lp93hjggrq4nrqwi78nyx3ls5")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -4232,6 +4306,8 @@ Bioconductor.") ("r-motiv" ,r-motiv) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -4245,14 +4321,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) + "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -4260,12 +4336,16 @@ type and symbol colors.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) + ("r-delayedarray" ,r-delayedarray) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) + ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) + ("r-rhdf5" ,r-rhdf5) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -4276,14 +4356,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.10.4") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in")))) + "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -4323,14 +4403,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb")))) + "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -4372,14 +4452,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) + "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -4389,6 +4469,8 @@ annotations and ontologies.") ("r-gplots" ,r-gplots) ("r-gtools" ,r-gtools) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -4402,14 +4484,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) + "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) @@ -4427,14 +4509,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) + "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -4452,14 +4534,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) + "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -4483,6 +4565,8 @@ text files).") ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -4493,14 +4577,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) + "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -4512,6 +4596,8 @@ investigation using RNA-seq data.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -4530,14 +4616,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.28.1") + (version "4.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) + "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -4569,14 +4655,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw")))) + "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4589,6 +4675,8 @@ visualization with image data.") ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -4601,20 +4689,22 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) + "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -4628,14 +4718,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) + "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -4653,6 +4743,8 @@ genomic categories and to add self-defined graphics in the plot.") ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -4665,33 +4757,42 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) + "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-corrplot" ,r-corrplot) ("r-dendextend" ,r-dendextend) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) + ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) ("r-lsei" ,r-lsei) + ("r-magrittr" ,r-magrittr) ("r-pmcmr" ,r-pmcmr) + ("r-pracma" ,r-pracma) ("r-reshape2" ,r-reshape2) ("r-somaticsignatures" ,r-somaticsignatures) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -4705,14 +4806,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) + "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4741,14 +4842,14 @@ gene-specific bidning is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) + "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4769,14 +4870,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) + "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) @@ -4791,14 +4892,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) + "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4808,6 +4909,8 @@ chips with the MAQC reference datasets.") ("r-iterators" ,r-iterators) ("r-minfi" ,r-minfi) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -4822,14 +4925,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) + "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4843,6 +4946,8 @@ groups.") ("r-quantro" ,r-quantro) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-readr" ,r-readr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -4857,14 +4962,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) + "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4886,14 +4991,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) + "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs @@ -4906,6 +5011,8 @@ sites and alignments obtained from standard RNA-seq experiments.") ("r-matrixstats" ,r-matrixstats) ("r-pracma" ,r-pracma) ("r-roar" ,r-roar))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -4923,14 +5030,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) + "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -4947,14 +5054,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.8.2") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g")))) + "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4964,14 +5071,16 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) - ("r-multtest" ,r-multtest) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -4984,20 +5093,22 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) + "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -5008,14 +5119,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) + "15l8f7ls2mwhsw68sr1k4r19hmdzjriibr5hpnfbanzj5x6yhdjq")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5028,6 +5139,8 @@ that arising from 16s metagenomic surveys.") ("r-purrr" ,r-purrr) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -5040,14 +5153,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) + "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -5061,14 +5174,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) + "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -5094,14 +5207,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) + "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -5110,6 +5223,8 @@ Currently only Affymetrix oligonucleotide analysis is supported.") ("r-ggplot2" ,r-ggplot2) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -5121,18 +5236,20 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) + "1z2dn0q3wcw8b9ibx388kh7p5km16i71sw9miqj3daw7g0v5bxp3")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -5144,16 +5261,24 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) + "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh")))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gridextra" ,r-gridextra) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -5166,14 +5291,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) + "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -5189,14 +5314,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) + "02chrzwccmazi7rdfpyriizhbgxyxlmprlw32w05wk54as6wrxv8")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -5207,6 +5332,8 @@ Infinium HumanMethylation 450k assay.") ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs) ("r-rsqlite" ,r-rsqlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -5219,14 +5346,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) + "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5249,18 +5376,20 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) + "06y1qp915dlwjdi2fs3344sgya55pcv07f3i61y0cxb0bhbcgvrz")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -5272,14 +5401,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) + "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -5297,6 +5426,8 @@ alignment tool.") ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -5313,14 +5444,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) + "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -5339,6 +5470,8 @@ interpretation.") `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-sgseq" ,r-sgseq))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -5351,14 +5484,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) + "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs @@ -5384,6 +5517,8 @@ index.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -5396,14 +5531,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) + "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -5425,6 +5560,8 @@ quantification of genomic regions of interest.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -5437,14 +5574,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) + "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -5466,14 +5603,14 @@ routines to analyse the resulting networks and their natural projections.") (define-public r-birta (package (name "r-birta") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 - "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) + "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5495,14 +5632,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) + "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -5516,6 +5653,8 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") ("r-qqman" ,r-qqman) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -5530,14 +5669,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.18.8") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) + "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5568,14 +5707,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl")))) + "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5601,14 +5740,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) + "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5624,6 +5763,8 @@ datasets.") ("r-reshape2" ,r-reshape2) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -5640,17 +5781,19 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.0.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy")))) + "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -5664,14 +5807,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) + "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -5690,14 +5833,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) + "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -5715,16 +5858,27 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "1.8.0") + (version "2.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) + "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-rprotobuflib" ,r-rprotobuflib))) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -5735,14 +5889,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "1.52.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) + "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -5751,7 +5905,11 @@ interact with gated cytometry data.") ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rprotobuflib" ,r-rprotobuflib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -5762,14 +5920,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) + "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -5788,14 +5946,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) + "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (inputs @@ -5809,6 +5967,8 @@ change point detection.") ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -5819,14 +5979,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50")))) + "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -5835,6 +5995,7 @@ manipulation of flow cytometry data.") ("r-flowworkspace" ,r-flowworkspace) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) + ("r-hexbin" ,r-hexbin) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) @@ -5855,14 +6016,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) + "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -5875,6 +6036,8 @@ statistics to the plot.") ("r-latticeextra" ,r-latticeextra) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -5884,14 +6047,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) + "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -5910,7 +6073,8 @@ statistics to the plot.") (inputs `(("gsl" ,gsl))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -5923,14 +6087,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "1.8.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) + "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -5939,8 +6103,10 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) #t))))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -5951,14 +6117,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "3.34.1") + (version "4.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn")))) + "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -5970,21 +6136,24 @@ for other R packages to compile and link against.") ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) + ("r-ggplot2" ,r-ggplot2) ("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-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -5999,14 +6168,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "3.44.0") + (version "4.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) + "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -6035,14 +6204,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "1.24.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) + "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -6067,6 +6236,8 @@ package.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rrcov" ,r-rrcov))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -6077,14 +6248,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "1.12.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz")))) + "0zpq2j4y9i5lls1kj2w4spl8qjp3076idsr2a2rjvy1fykzlp01q")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -6103,15 +6274,17 @@ sequential way to mimic the manual gating strategy.") ("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-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-runit" ,r-runit) + ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) ("r-yaml" ,r-yaml))) (native-inputs @@ -6126,14 +6299,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) + "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -6156,14 +6329,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.10.9") + (version "6.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig")))) + "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -6200,14 +6373,14 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm")))) + "0nmx04qybzf6nhfngmdxwpbbz9x32v34mbnpg8jq7a2cgchzsj9s")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -6245,14 +6418,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) + "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -6263,6 +6436,8 @@ data, to only emphasize the data that actually matters.") ("r-gseabase" ,r-gseabase) ("r-r-utils" ,r-r-utils) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -6280,14 +6455,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.4.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld")))) + "0n78lf5hz6zzl550dbf4imis43pv91zicfff8y4lspckljhz9z75")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6390,17 +6565,19 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) + "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -6411,14 +6588,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) + "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs @@ -6459,14 +6636,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) + "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -6496,14 +6673,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) + "00hggma0i15w03xi9jr02v2593jbqkcxyfcvpp7mdzrshn99m9p6")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -6533,6 +6710,8 @@ metrics, with methods for objects produced by the @code{methylumi} and `(("lz4" ,lz4) ("xz" ,xz) ("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -6553,14 +6732,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) + "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -6581,14 +6760,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) + "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -6647,14 +6826,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) + "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -6672,14 +6851,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) + "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -6698,6 +6877,8 @@ format.") ("r-seqinr" ,r-seqinr) ("r-stringr" ,r-stringr) ("r-wmtsa" ,r-wmtsa))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -6718,14 +6899,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) + "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -6745,6 +6926,8 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") ("r-tidyr" ,r-tidyr) ("r-vegan" ,r-vegan) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -6757,14 +6940,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) + "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -6863,14 +7046,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g")))) + "1rn655qq7dshbk1dd41n7y2hfz8498jxd2j4rk7p8hrikd3s32dm")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -6891,6 +7074,8 @@ arrays based on fast wavelet-based functional models.") ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -6905,14 +7090,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) + "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -6939,14 +7124,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) + "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -7030,14 +7215,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) + "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -7052,14 +7237,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) + "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs @@ -7077,14 +7262,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) + "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -7103,14 +7288,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) + "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -7127,19 +7312,21 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) + "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-poibin" ,r-poibin))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -7155,14 +7342,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) + "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -7183,14 +7370,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) + "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -7205,14 +7392,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) + "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) @@ -7229,14 +7416,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) + "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -7259,19 +7446,21 @@ networks and estimated fluxes can be visualized with hypergraphs.") (define-public r-bigmemoryextras (package (name "r-bigmemoryextras") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmemoryExtras" version)) (sha256 (base32 - "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) + "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g")))) (properties `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs `(("r-bigmemory" ,r-bigmemory))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -7291,18 +7480,19 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs")))) + "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-delayedarray" ,r-delayedarray) + ("r-dplyr" ,r-dplyr) ("r-ggally" ,r-ggally) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) @@ -7317,6 +7507,7 @@ a file-backed matrix with factor properties.") ("r-shinycssloaders" ,r-shinycssloaders) ("r-shinydashboard" ,r-shinydashboard) ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7332,14 +7523,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.38.0") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) + "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -7356,6 +7547,8 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) ("r-rsvg" ,r-rsvg))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -7371,14 +7564,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) + "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -7406,14 +7599,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) + "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -7421,6 +7614,8 @@ available bioactivity data.") ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -7436,14 +7631,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) + "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -7463,14 +7658,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) + "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -7482,6 +7677,8 @@ symbols).") ("r-graphite" ,r-graphite) ("r-igraph" ,r-igraph) ("r-reactome-db" ,r-reactome-db))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -7493,14 +7690,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) + "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -7517,14 +7714,14 @@ microarray data.") (define-public r-bioccasestudies (package (name "r-bioccasestudies") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCaseStudies" version)) (sha256 (base32 - "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) + "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix")))) (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) @@ -7539,14 +7736,14 @@ monograph.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) + "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -7564,14 +7761,14 @@ different graph related packages produced by Bioconductor.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) + "18d6kjfavy5b769gpkblihdkz2nz2hsgyjki8mp1sywi0ik08ncd")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -7582,6 +7779,8 @@ different graph related packages produced by Bioconductor.") ("r-curl" ,r-curl) ("r-rappdirs" ,r-rappdirs) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -7596,14 +7795,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.6") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi")))) + "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -7631,14 +7830,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) + "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -7664,6 +7863,8 @@ rownames.") ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -7674,20 +7875,22 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) + "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-gseabase" ,r-gseabase) ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -7701,14 +7904,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.4.6") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a")))) + "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -7751,14 +7954,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.0.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) + "14dmkc878lskbm001kgjyqmrwnn6s032z4h64f617f1xd9zx9wrj")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -7769,6 +7972,8 @@ analytics on packages.") ("r-rlang" ,r-rlang) ("r-rtracklayer" ,r-rtracklayer) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -7784,14 +7989,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6")))) + "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -7817,14 +8022,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) + "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -7836,3 +8041,49 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") "This package provides a collection of software tools for calculating distance measures.") (license license:artistic2.0))) + +(define-public r-pcatools + (package + (name "r-pcatools") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PCAtools" version)) + (sha256 + (base32 + "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc")))) + (properties `((upstream-name . "PCAtools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-bh" ,r-bh) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-cowplot" ,r-cowplot) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dqrng" ,r-dqrng) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/kevinblighe/PCAtools") + (synopsis "PCAtools: everything Principal Components Analysis") + (description + "@dfn{Principal Component Analysis} (PCA) extracts the fundamental +structure of the data without the need to build any model to represent it. +This \"summary\" of the data is arrived at through a process of reduction that +can transform the large number of variables into a lesser number that are +uncorrelated (i.e. the 'principal components'), while at the same time being +capable of easy interpretation on the original data. PCAtools provides +functions for data exploration via PCA, and allows the user to generate +publication-ready figures. PCA is performed via @code{BiocSingular}; users +can also identify an optimal number of principal components via different +metrics, such as the elbow method and Horn's parallel analysis, which has +relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high +dimensional mass cytometry data.") + (license license:gpl3))) |