diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 888 |
1 files changed, 286 insertions, 602 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4976f6183b..c3b1ec6678 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4160,6 +4160,7 @@ VCF.") ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException #:tests? #f #:jdk ,icedtea-8 + #:ant ,ant/java8 ;; This is only used for tests. #:make-flags (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") @@ -4237,7 +4238,7 @@ VCF.") `(("java-snappy-1" ,java-snappy-1) ("java-commons-jexl-2" ,java-commons-jexl-2) ("java-cofoja" ,java-cofoja) - ("ant" ,ant) ; for bzip2 support at runtime + ("ant" ,ant/java8) ; for bzip2 support at runtime ("zlib" ,zlib))) (native-inputs `(("ant-apache-bcel" ,ant-apache-bcel) @@ -7136,14 +7137,14 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g")))) + "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -7164,14 +7165,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp")))) + "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -7202,14 +7203,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl")))) + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7247,14 +7248,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw")))) + "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -7279,14 +7280,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy")))) + "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -7302,14 +7303,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.50.1") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j")))) + "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7331,14 +7332,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b")))) + "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -7362,14 +7363,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9")))) + "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -7393,14 +7394,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d")))) + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7413,6 +7414,7 @@ testing and other simple calculations.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) ("r-hwriter" ,r-hwriter) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) @@ -7435,14 +7437,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.22.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2")))) + "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7458,6 +7460,7 @@ ungapped alignment formats.") ("r-ggplot2" ,r-ggplot2) ("r-go-db" ,r-go-db) ("r-gostats" ,r-gostats) + ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-pheatmap" ,r-pheatmap) @@ -7488,14 +7491,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb")))) + "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -7721,13 +7724,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.56.2") + (version "1.58.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w")))) + "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7749,13 +7752,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.16.1") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7")))) + "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7777,13 +7780,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny")))) + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7826,13 +7829,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.26.1") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb")))) + "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7853,13 +7856,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.22.2") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d")))) + "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7905,13 +7908,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.24.2") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd")))) + "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7935,13 +7938,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.30.3") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic")))) + "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7963,17 +7966,15 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw")))) + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) (properties `((upstream-name . "VariantAnnotation"))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) @@ -7985,6 +7986,7 @@ CAGE.") ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) @@ -8002,13 +8004,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.44.3") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6")))) + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -8021,13 +8023,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc")))) + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -8057,13 +8059,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1")))) + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -8088,13 +8090,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp")))) + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -8110,13 +8112,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.50.3") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3")))) + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -8139,13 +8141,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.44.1") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz")))) + "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8157,7 +8159,8 @@ annotation data packages using SQLite data storage.") ("r-progress" ,r-progress) ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml))) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biomaRt") @@ -8176,13 +8179,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.22.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g")))) + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -8203,13 +8206,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8")))) + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -8230,13 +8233,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq")))) + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8250,8 +8253,6 @@ biological sequences or sets of sequences.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") "")) #t))))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) @@ -8275,13 +8276,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.14.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v")))) + "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -8290,7 +8291,7 @@ tab-delimited (tabix) files.") ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats))) + ("r-matrixgenerics" ,r-matrixgenerics))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DelayedArray") @@ -8308,13 +8309,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw")))) + "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8326,6 +8327,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8341,13 +8343,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d")))) + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -8374,13 +8376,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf")))) + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) (build-system r-build-system) (arguments `(#:phases @@ -8407,7 +8409,8 @@ alignments.") ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description @@ -8421,13 +8424,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.40.1") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z")))) + "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8488,13 +8491,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr")))) + "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8521,13 +8524,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6")))) + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -8552,13 +8555,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h")))) + "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -8572,13 +8575,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0f1yvx2ri1557rzjx08q5bgml1cvkm8hjl8xn1qi4rjs64sy6mci")))) + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8599,13 +8602,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1cy8kqwddiha5jy6nda1al956i4wncbgjkrxwijdb08cmka2sfwh")))) + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8647,7 +8650,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.14.0") + (version "1.22.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8657,7 +8660,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7")))) + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. @@ -8675,16 +8678,18 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.54.3") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "09kkxir305fv8z2yyihvspkrzclxbw1cx5mvhfkrhl10rap6662j")))) + "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -8723,13 +8728,13 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0j1l052jb2cwc1nifxzwknc9csagf4f2d092zs0i95dz0rma89l0")))) + "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8765,14 +8770,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "186r7icrkzrni1c4n33ip7dlsfgys7hnqf0simvxrpl3yhh3ygdi")))) + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8780,9 +8785,8 @@ secondary structure and comparative analysis in R.") (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) @@ -8797,14 +8801,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0p858xxfv79yc8b3lq58zl9f00irvbn3czsd8wdi5040xg42m402")))) + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8813,8 +8817,6 @@ of other R packages who wish to make use of HTSlib.") ("r-rcpp" ,r-rcpp) ("r-rhtslib" ,r-rhtslib) ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bamsignals") @@ -8829,13 +8831,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0f812pgv3ys1zv4n9sqkgm01hj4cdd0i0h85dqbhkwd94zl6cavl")))) + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -8929,33 +8931,40 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "2.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm")))) + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) ;; These two packages are suggested packages ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomicranges" ,r-genomicranges) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) ("r-nmf" ,r-nmf) - ("r-plyr" ,r-plyr) ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-cowplot" ,r-cowplot) - ("r-ggdendro" ,r-ggdendro) + ("r-purrr" ,r-purrr) ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) ("r-variantannotation" ,r-variantannotation))) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") @@ -9034,13 +9043,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1x9959lkjl2h869rgd1b30q1idxzjkr1fyqbpndqk3kbi4q2gr40")))) + "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -9055,21 +9064,57 @@ provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "1jvnss44liapbc6hk93yg1gknv0ahd5x86dydqiwq9l65jd03psq")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.3") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf")))) + "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) - (inputs - `(("zlib" ,zlib))) + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/rhdf5") @@ -9087,13 +9132,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "18kh1xrhpwb48s1qj4f1v8af3jmw49pnbp5afi2myn9894hxg0cs")))) + "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -9434,14 +9479,14 @@ manipulate and analyze genetic variants.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "0lh859s0aq73vac1phcgagf6n000qgq2xsk0bmfr61n5swifml2a")))) + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9486,14 +9531,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0c36wpv0rygkbqpf3dwh5xmc3lr7p8lrdzsq2fbbpw04skl6i7m2")))) + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9526,13 +9571,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1qr13d2712ypbn96ijic2z5adr5dsd61kzscx7shw6vyj360rlm5")))) + "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9557,8 +9602,6 @@ number detection tools.") ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes - (inputs - `(("zlib" ,zlib))) (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -9575,14 +9618,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.36.0") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0xa1lm0k1a6nig90mab6xh4gln88rbs5l1cdr6ik6agg7jhs7ji4")))) + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) @@ -9638,14 +9681,14 @@ trait.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "14xzdh7vxss8vmrw91hcwrszdn3ikm71mah8875b2lkrkrfzbl73")))) + "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9658,14 +9701,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.22.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm")) + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) (modules '((guix build utils))) (snippet '(begin @@ -9680,14 +9723,19 @@ proteomics packages.") (lambda _ (substitute* "src/Makevars" (("\\./boost/libs.*") "") - (("ARCH_OBJS=" line) + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) (string-append line - "\nARCH_LIBS=-lboost_system -lboost_regex \ + "\nBOOST_LIBS=-lboost_system -lboost_regex \ -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.22.0. + ;; mzR version 2.24.1. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9714,14 +9762,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q")))) + "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9738,14 +9786,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc")))) + "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9766,14 +9814,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.56.0") + (version "3.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58")))) + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9802,14 +9850,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5")))) + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9818,7 +9866,6 @@ and specific in detecting differential transcription.") ("r-iterators" ,r-iterators) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -9834,14 +9881,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni")))) + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9864,14 +9911,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l")))) + "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9909,30 +9956,43 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc")))) + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) ("r-data-table" ,r-data-table) ("r-doparallel" ,r-doparallel) ("r-dplyr" ,r-dplyr) ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) ("r-r-cache" ,r-r-cache) ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -9948,14 +10008,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc")))) + "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -10006,14 +10066,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4")))) + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -10024,7 +10084,6 @@ distribution.") ("r-biocmanager" ,r-biocmanager) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) - ("r-deseq" ,r-deseq) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) @@ -10047,14 +10106,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.26.3") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3")))) + "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -10074,14 +10133,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5")))) + "1950x654ffqx53b154kbph808zdh2xm5vmj9vzmc5nxc28fi2z5g")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10115,14 +10174,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63")))) + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -10145,14 +10204,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1")))) + "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -10171,14 +10230,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.38.3") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p")))) + "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10202,14 +10261,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4")))) + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10219,6 +10278,7 @@ analysis using other methods.") ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) @@ -10235,25 +10295,30 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.4.3") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q")))) + "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) + `(("r-cairo" ,r-cairo) + ("r-circlize" ,r-circlize) ("r-clue" ,r-clue) ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) ("r-getoptlong" ,r-getoptlong) ("r-globaloptions" ,r-globaloptions) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page @@ -10269,14 +10334,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb")))) + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10298,14 +10363,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g")))) + "04il99gcrqzakvc0bxchdp9gghkn1sp9lpiian0iz4y7r67z3wpy")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10343,14 +10408,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw")))) + "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -10375,14 +10440,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh")))) + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10414,401 +10479,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - -(define-public r-gqtlbase - (package - (name "r-gqtlbase") - (version "1.20.4") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLBase" version)) - (sha256 - (base32 - "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41")))) - (properties `((upstream-name . "gQTLBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLBase") - (synopsis "Infrastructure for eQTL, mQTL and similar studies") - (description - "The purpose of this package is to simplify the storage and interrogation -of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, -and more.") - (license license:artistic2.0))) - -(define-public r-snpstats - (package - (name "r-snpstats") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "snpStats" version)) - (sha256 - (base32 - "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq")))) - (properties `((upstream-name . "snpStats"))) - (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/snpStats") - (synopsis "Methods for SNP association studies") - (description - "This package provides classes and statistical methods for large -@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends -the earlier snpMatrix package, allowing for uncertainty in genotypes.") - (license license:gpl3))) - -(define-public r-homo-sapiens - (package - (name "r-homo-sapiens") - (version "1.3.1") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "Homo.sapiens_" - version ".tar.gz")) - (sha256 - (base32 - "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) - (properties - `((upstream-name . "Homo.sapiens"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/Homo.sapiens/") - (synopsis "Annotation package for the Homo.sapiens object") - (description - "This package contains the Homo.sapiens object to access data from -several related annotation packages.") - (license license:artistic2.0))) - -(define-public r-erma - (package - (name "r-erma") - (version "1.4.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "erma" version)) - (sha256 - (base32 - "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/erma") - (synopsis "Epigenomic road map adventures") - (description - "The epigenomics road map describes locations of epigenetic marks in DNA -from a variety of cell types. Of interest are locations of histone -modifications, sites of DNA methylation, and regions of accessible chromatin. -This package presents a selection of elements of the road map including -metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines -by Ernst and Kellis.") - (license license:artistic2.0))) - -(define-public r-ldblock - (package - (name "r-ldblock") - (version "1.18.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ldblock" version)) - (sha256 - (base32 - "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/ldblock") - (synopsis "Data structures for linkage disequilibrium measures in populations") - (description - "This package defines data structures for @dfn{linkage -disequilibrium} (LD) measures in populations. Its purpose is to simplify -handling of existing population-level data for the purpose of flexibly -defining LD blocks.") - (license license:artistic2.0))) - -(define-public r-gqtlstats - (package - (name "r-gqtlstats") - (version "1.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLstats" version)) - (sha256 - (base32 - "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7")))) - (properties `((upstream-name . "gQTLstats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLstats") - (synopsis "Computationally efficient analysis for eQTL and allied studies") - (description - "This package provides tools for the computationally efficient analysis -of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. -The software in this package aims to support refinements and functional -interpretation of members of a collection of association statistics on a -family of feature/genome hypotheses.") - (license license:artistic2.0))) - -(define-public r-gviz - (package - (name "r-gviz") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Gviz" version)) - (sha256 - (base32 - "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a")))) - (properties `((upstream-name . "Gviz"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Gviz") - (synopsis "Plotting data and annotation information along genomic coordinates") - (description - "Genomic data analyses requires integrated visualization of known genomic -information and new experimental data. Gviz uses the biomaRt and the -rtracklayer packages to perform live annotation queries to Ensembl and UCSC -and translates this to e.g. gene/transcript structures in viewports of the -grid graphics package. This results in genomic information plotted together -with your data.") - (license license:artistic2.0))) - -(define-public r-gwascat - (package - (name "r-gwascat") - (version "2.20.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gwascat" version)) - (sha256 - (base32 - "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gwascat") - (synopsis "Tools for data in the EMBL-EBI GWAS catalog") - (description - "This package provides tools for representing and modeling data in the -EMBL-EBI GWAS catalog.") - (license license:artistic2.0))) - -(define-public r-sushi - (package - (name "r-sushi") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Sushi" version)) - (sha256 - (base32 - "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb")))) - (properties `((upstream-name . "Sushi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) - (home-page "https://bioconductor.org/packages/Sushi") - (synopsis "Tools for visualizing genomics data") - (description - "This package provides flexible, quantitative, and integrative genomic -visualizations for publication-quality multi-panel figures.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -11368,21 +11038,23 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") #t))))) (native-inputs `(("samtabix" - ,(origin - (method git-fetch) - (uri (git-reference - (url "http://genome-source.cse.ucsc.edu/samtabix.git") - (commit "10fd107909c1ac4d679299908be4262a012965ba"))) - (sha256 - (base32 - "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) + ,(let ((commit "10fd107909c1ac4d679299908be4262a012965ba")) + (origin + (method git-fetch) + (uri (git-reference + (url "http://genome-source.cse.ucsc.edu/samtabix.git") + (commit commit))) + (file-name (git-file-name "samtabix" (string-take commit 7))) + (sha256 + (base32 + "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))) (inputs `(("zlib" ,zlib) ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) ("mariadb-dev" ,mariadb "dev") - ("openssl" ,openssl-1.0))) + ("openssl" ,openssl))) (home-page "https://genome.cse.ucsc.edu/index.html") (synopsis "Assorted bioinformatics utilities") (description "This package provides the kentUtils, a selection of @@ -12676,7 +12348,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.43") + (version "0.0.51") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12684,7 +12356,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0426i31b7mqqkbss5dgrvf5prkj4z1qrd7yrpd27vybs01xhdlks")))) + "0bb6hzpl0qq0jd57pgd1m5ns547rfipr6071a4m12vxlm4nlpi5q")))) (build-system gnu-build-system) ;; parts of the tests rely on access to the network (arguments '(#:tests? #f)) @@ -12696,23 +12368,30 @@ expression report comparing samples in an easily configurable manner.") ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-chipseq" ,r-chipseq) + ("r-corrplot" ,r-corrplot) ("r-data-table" ,r-data-table) + ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gprofiler2" ,r-gprofiler2) + ("r-heatmaply" ,r-heatmaply) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-rmarkdown" ,r-rmarkdown) ("r-rsamtools" ,r-rsamtools) + ("r-rsubread" ,r-rsubread) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) - ("r-jsonlite" ,r-jsonlite) - ("r-heatmaply" ,r-heatmaply) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-ggplot2" ,r-ggplot2) - ("r-plotly" ,r-plotly) - ("r-rmarkdown" ,r-rmarkdown) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("python-magic" ,python-magic) @@ -12813,7 +12492,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.4") + (version "1.1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12821,7 +12500,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9")))) + "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) @@ -13043,21 +12722,26 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")))) + "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")) + (patches (search-patches "minimap2-aarch64-support.patch")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none #:make-flags - (list "CC=gcc" + (list (string-append "CC=" ,(cc-for-target)) (let ((system ,(or (%current-target-system) (%current-system)))) (cond - ((string-prefix? "x86_64" system) - "all") - ((or (string-prefix? "armhf" system) - (string-prefix? "aarch64" system)) - "arm_neon=1") - (else "sse2only=1")))) + ((string-prefix? "x86_64" system) + "all") + ((or (string-prefix? "i586" system) + (string-prefix? "i686" system)) + "sse2only=1") + ((string-prefix? "armhf" system) + "arm_neon=1") + ((string-prefix? "aarch64" system) + "aarch64=1") + (else "")))) #:phases (modify-phases %standard-phases (delete 'configure) |