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-rw-r--r--gnu/packages/bioinformatics.scm222
1 files changed, 123 insertions, 99 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0b8056179..fa35531868 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -602,15 +602,19 @@ e.g. microbiome samples, genomes, metagenomes.")
(map (compose package-transitive-target-inputs cadr) inputs))))))
(package
(name "bioperl-minimal")
- (version "1.6.924")
+ (version "1.7.0")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/bioperl/bioperl-live/"
+ "archive/release-"
+ (string-map (lambda (c)
+ (if (char=? c #\.)
+ #\- c)) version)
+ ".tar.gz"))
(sha256
(base32
- "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
+ "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
(build-system perl-build-system)
(arguments
`(#:phases
@@ -5190,14 +5194,14 @@ data types as well.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "00wnhbjp5i6a5vyvlq4f5hs8qngjxz7fm869kla1spmd0dp2ynsy"))))
+ "1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -5216,14 +5220,14 @@ microarrays.")
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "0lvrywl0251g4y0h0qlgkbg4l83ja5544c85z1wj30qxiy77iqc2"))))
+ "1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -5241,14 +5245,14 @@ microarrays.")
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.54.2")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "1hmz6as0njvrsrdbgmk72jyclnnqvfdvp6kqv456h43ldq2ajfv5"))))
+ "1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -5267,14 +5271,14 @@ high-throughput sequencing experiments.")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.12.4")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx"))))
+ "0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(arguments
@@ -5312,14 +5316,14 @@ distribution.")
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.14.2")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "1vkdd1qdv5g680ipw4vwjvn52xn66xpg6ngmwyknz77ckxnnpf4q"))))
+ "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@@ -5328,6 +5332,7 @@ distribution.")
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-dbi" ,r-dbi)
+ ("r-rcurl" ,r-rcurl)
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-xml" ,r-xml)))
@@ -5341,14 +5346,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.48.1")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "1k82zcbyfx3p9hc8r0hwq73krbhakjan8fgbfr6w8z2crfkv3zmz"))))
+ "1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs `(("r-graph" ,r-graph)))
@@ -5362,14 +5367,14 @@ the graph algorithms contained in the Boost library.")
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.34.1")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "1mvgja8malrnbzfakzjl5mmi7g080kj8zgxwc5964hcmn33i937j"))))
+ "0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
@@ -5389,14 +5394,14 @@ Enrichment Analysis} (GSEA).")
(define-public r-category
(package
(name "r-category")
- (version "2.38.0")
+ (version "2.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "0c8px9ar589f3iqkbk9vfhwj30dpnxj81h8sfq20cl1cbmcx2a04"))))
+ "16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
@@ -5420,14 +5425,14 @@ analysis.")
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.38.1")
+ (version "2.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "1hhw6vqr8f3g4jzq0v8f2za0r1h117j5s6av87zxs41cv7dq1wb3"))))
+ "0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
@@ -5450,14 +5455,14 @@ testing and other simple calculations.")
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg"))))
+ "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@@ -5492,14 +5497,14 @@ ungapped alignment formats.")
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.6.4")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m"))))
+ "0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
@@ -5538,14 +5543,14 @@ annotation infrastructure.")
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "1l9mcyzyc548114ysb9r0q7hgzw3yy7gpiahrzkzj6hblc4f1jyp"))))
+ "0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
@@ -5852,13 +5857,13 @@ barplots or heatmaps.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.18.0")
+ (version "0.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6"))))
+ "06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@@ -5872,13 +5877,13 @@ packages.")
(define-public r-biocinstaller
(package
(name "r-biocinstaller")
- (version "1.22.3")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocInstaller" version))
(sha256
(base32
- "02qkfq6f2b7v9klri6d1nv21r54bywv1zd5x47ka0jhhp946cqpr"))))
+ "0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn"))))
(properties
`((upstream-name . "BiocInstaller")))
(build-system r-build-system)
@@ -6032,13 +6037,13 @@ that accept short and long options.")
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip"))))
+ "1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh"))))
(properties
`((upstream-name . "DNAcopy")))
(build-system r-build-system)
@@ -6054,13 +6059,13 @@ abnormal copy number.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.10.3")
+ (version "0.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "09lrvy3d5q58hsgw9as4hyyx07k1vyy2zjn3xsvhyfd97yk6w6lv"))))
+ "0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -6081,14 +6086,14 @@ S4Vectors package itself.")
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "3.3-1")
+ (version "3.3-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "1al83y6m7739dz2j895yihksm0s5l45ialid4yw911ylbg3w6cm1"))))
+ "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
@@ -6106,13 +6111,13 @@ utilities for sequence data management under the ACNUC system.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.6.1")
+ (version "2.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "06pyam3bjjfw2m3l86rda503lsz2jcg645lcnhvrz6qi0nv359yg"))))
+ "0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -6135,13 +6140,13 @@ possible.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.8.7")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1x96468bbjx7z3ikp1dgr2krnz9pwx86vmssfbfrsikaxfs4q829"))))
+ "0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -6161,17 +6166,18 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.14.0")
+ (version "3.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "14vrygy7rz5ngaap4kgkvr3j18y5l6m742n79h68plk6iqgmsskn"))))
+ "1qr20j55m35dwzqyzzmla69gk5bzff8v1v2qjh7yd3362wq1ch49"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-limma" ,r-limma)))
+ `(("r-limma" ,r-limma)
+ ("r-locfit" ,r-locfit)))
(home-page "http://bioinf.wehi.edu.au/edgeR")
(synopsis "EdgeR does empirical analysis of digital gene expression data")
(description "This package can do differential expression analysis of
@@ -6186,27 +6192,33 @@ CAGE.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.18.7")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "002kif2c66wbcng953m3g1jys7w1lgz7hh3zsk4jlnhc20jdv1vj"))))
+ "1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-dbi" ,r-dbi)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
("r-zlibbioc" ,r-zlibbioc)))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/VariantAnnotation")
@@ -6218,13 +6230,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.28.21")
+ (version "3.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1dvisifd2rr7s1rrsqj5vrv2qcg4la4yi2ajbn0zkk5z81ffxv9f"))))
+ "0d8wp7b7nymawf4czwsg27k4c61i4ij2lhv7phi6cb3hdd8c76yf"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -6237,13 +6249,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.12.1")
+ (version "0.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1kydy9f5y0ihn2mbkamr1kh0g1d3g1k9d7s4i09qgw9ysr6j414v"))))
+ "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
@@ -6273,19 +6285,21 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.24.3")
+ (version "1.26.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "098a34hfgb5z120v6wpl5nv8v61nm65yg6xq0j7i9bigvxr7apg2"))))
+ "039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/GenomicRanges")
(synopsis "Representation and manipulation of genomic intervals")
@@ -6300,13 +6314,13 @@ manipulating genomic intervals and variables defined along a genome.")
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.32.0")
+ (version "2.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i"))))
+ "0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
@@ -6322,13 +6336,13 @@ on Bioconductor or which replace R functions.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.34.4")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "1k3gfsjrivc7467vg0h705hh4dvzgdhknz62j7zmfxm67qk9r8rq"))))
+ "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -6349,13 +6363,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.28.0")
+ (version "2.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v"))))
+ "1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -6379,13 +6393,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.6.6")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1l39zmvhjlvlczrk5wal4y2s4g0b2kmaczgq5biah9qn45y474mw"))))
+ "0vz23i14f7wjygr5d4y1hp8ki6l6igwcsjscfpr6dcigmknyi55c"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -6403,13 +6417,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.40.2")
+ (version "2.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "153rfws5sdha324p1nv7jp75ip6ny0f62jzhqcvs46l85h3i8zgh"))))
+ "08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -6429,13 +6443,13 @@ biological sequences or sets of sequences.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.24.0")
+ (version "1.26.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb"))))
+ "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@@ -6473,13 +6487,13 @@ files.")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.2.3")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "0c43fsrha886sd0diislnlf8r5h5x7fbhphkzcm0rw3k2jz8wlyk"))))
+ "1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -6502,13 +6516,13 @@ samples.")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.8.4")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1cccvalmm83ilk1kpq31ll8kdy9xclsr4pm4mlcc7bmp0rwkd2p2"))))
+ "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@@ -6535,13 +6549,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.32.2")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "190767zpwc7maqjpy0x5bpkm0jp1vfawy9991fifw0mc634cjkga"))))
+ "0mix5k75j70mwplbdipqw71n8qic75ny6y8w2f5jj0pqg1k0327d"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -6580,13 +6594,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.24.5")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "17qpisdgqyjz2mnaiwc4dx7dg11pwq3mkvmkah9zn07g9rhh8f7p"))))
+ "0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -6621,7 +6635,7 @@ extracting the desired features in a convenient format.")
(define-public r-go-db
(package
(name "r-go-db")
- (version "3.3.0")
+ (version "3.4.0")
(source (origin
(method url-fetch)
(uri (string-append "http://www.bioconductor.org/packages/"
@@ -6629,7 +6643,7 @@ extracting the desired features in a convenient format.")
version ".tar.gz"))
(sha256
(base32
- "0x2hkbhg9d8waw32hdn05887vv3zbs5aqff3mf5vfyzvl7xhgxy0"))))
+ "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl"))))
(properties
`((upstream-name . "GO.db")))
(build-system r-build-system)
@@ -6645,13 +6659,13 @@ information about the latest version of the Gene Ontologies.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.50.0")
+ (version "1.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi"))))
+ "0g3dk5vsdp489fmyg8mifczmzgqrjlakkkr8i96dj15gghp3l135"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -6664,18 +6678,19 @@ information about the latest version of the Gene Ontologies.")
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.24.0")
+ (version "2.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar"))))
+ "0j6sgvam4lk9348ag6pypcbkv93x4fk0di8ivhr23mz2s2yqzwrx"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dbi" ,r-dbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-go-db" ,r-go-db)
@@ -6695,13 +6710,13 @@ dependencies between GO terms can be implemented and applied.")
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.40.1")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "0zmlzlcwairka59is5wmkh6knh6j4d328z9fsw3v91fx6gavjl2n"))))
+ "0hxwc02h5mzhkrk60d1jmlsfjf0ai9jxdc0128kj1sg4r2k1q94y"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
@@ -6725,13 +6740,13 @@ genome data packages and support for efficient SNP representation.")
(define-public r-impute
(package
(name "r-impute")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0"))))
+ "1164zvnikbjd0ybdn9xwn520rlmdjd824vmhnl83zgv3v9lzp9bm"))))
(inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
@@ -6745,13 +6760,13 @@ microarray data, using nearest neighbor averaging.")
(define-public r-seqpattern
(package
(name "r-seqpattern")
- (version "1.4.0")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "seqPattern" version))
(sha256
(base32
- "1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb"))))
+ "0lsa5pz36xapi3yiv78k3z286a5md5sm5g21pgfyg8zmhmkxr7y8"))))
(properties
`((upstream-name . "seqPattern")))
(build-system r-build-system)
@@ -6759,6 +6774,7 @@ microarray data, using nearest neighbor averaging.")
`(("r-biostrings" ,r-biostrings)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
("r-plotrix" ,r-plotrix)))
(home-page "http://bioconductor.org/packages/seqPattern")
(synopsis "Visualising oligonucleotide patterns and motif occurrences")
@@ -6771,13 +6787,13 @@ reference point and sorted by a user defined feature.")
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.4.2")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "017hxh3yhizlsswd2vw8504arkckrcgq5zraiw67lldq9wzs5qzg"))))
+ "1m4mz7wihj8yqivwkzw68div8ybk4rjsai3ffki7xp7sh21ax03y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
@@ -6793,11 +6809,17 @@ reference point and sorted by a user defined feature.")
("r-matrixstats" ,r-matrixstats)
("r-plotrix" ,r-plotrix)
("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
("r-readr" ,r-readr)
("r-reshape2" ,r-reshape2)
+ ("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
+ ("r-runit" ,r-runit)
+ ("r-s4vectors" ,r-s4vectors)
("r-seqpattern" ,r-seqpattern)))
+ (inputs
+ `(("zlib" ,zlib)))
(home-page "http://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
@@ -6814,7 +6836,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.4.2")
+ (version "1.6.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -6824,7 +6846,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "1zl7gg144fs7zfycsmq5492sm1bqy7l527xbc2zj04schd9wsan2"))))
+ "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
@@ -6946,14 +6968,14 @@ annotations for the genome of the model mouse Mus musculus.")
(define-public r-seqlogo
(package
(name "r-seqlogo")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqLogo" version))
(sha256
(base32
- "01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb"))))
+ "18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/seqLogo")
@@ -7157,14 +7179,14 @@ Biostrings objects.")
(define-public r-motifrg
(package
(name "r-motifrg")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifRG" version))
(sha256
(base32
- "1ds22paqc0923y6z1fy0arw0wxvvmglfvfgarhywv1qywhq68mbq"))))
+ "1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d"))))
(properties `((upstream-name . "motifRG")))
(build-system r-build-system)
(propagated-inputs
@@ -7209,13 +7231,13 @@ two-dimensional genome scans.")
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "zlibbioc" version))
(sha256
(base32
- "0m8l7zpx1l3qsk73k3ibkxxzzff938x3qhnwki1ymf3cnsg8cb36"))))
+ "0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq"))))
(properties
`((upstream-name . "zlibbioc")))
(build-system r-build-system)
@@ -7228,20 +7250,22 @@ libraries for systems that do not have these available via other means.")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.4.3")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "1wgpn9x8abjj7fc087pdavqc3fz0pl5xdh231mgjila18irwlhb3"))))
+ "1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
(propagated-inputs
`(("r-zlibbioc" ,r-zlibbioc)))
(inputs
`(("zlib" ,zlib)))
+ (native-inputs
+ `(("autoconf" ,autoconf)))
(home-page "https://github.com/nhayden/Rhtslib")
(synopsis "High-throughput sequencing library as an R package")
(description
@@ -7253,14 +7277,14 @@ of other R packages who wish to make use of HTSlib.")
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.4.3")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy"))))
+ "1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-29 12:46:22 +0000