diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 1132 |
1 files changed, 936 insertions, 196 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 987662fc89..314aaa4077 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -47,6 +47,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) @@ -81,10 +82,12 @@ #:use-module (gnu packages parallel) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) + #:use-module (gnu packages perl-check) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-web) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) @@ -107,18 +110,19 @@ (define-public r-ape (package (name "r-ape") - (version "4.1") + (version "5.0") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) + "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) - ("r-nlme" ,r-nlme))) + ("r-nlme" ,r-nlme) + ("r-rcpp" ,r-rcpp))) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -1579,7 +1583,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") "-2017-0621-source.tar.gz")) (sha256 (base32 - "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn")))) + "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -1839,7 +1843,7 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (define-public cutadapt (package (name "cutadapt") - (version "1.12") + (version "1.14") (source (origin (method url-fetch) (uri (string-append @@ -1848,7 +1852,7 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v")))) + "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd")))) (build-system python-build-system) (arguments `(#:phases @@ -2059,7 +2063,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.11") + (version "0.9.13") (source (origin (method url-fetch) (uri (string-append @@ -2068,7 +2072,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1yqil5531p35xkqa44x75vvq8s7w8kqjqn1p5hf1nh0d91j9ihby")))) + "1pi5ncqwmynqpmmp3j3lhnqrjhj34sr6wpmsgrpkv3wyxx22fv86")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -3562,9 +3566,7 @@ assembled metagenomic sequence.") (version "0.5.4") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/m/misopy/misopy-" - version ".tar.gz")) + (uri (pypi-uri "misopy" version)) (sha256 (base32 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) @@ -4128,7 +4130,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.8.2") + (version "3.11.0") (source (origin (method url-fetch) @@ -4137,7 +4139,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7")))) + "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) (build-system perl-build-system) (arguments `(#:phases @@ -4203,6 +4205,7 @@ partial genes, and identifies translation initiation sites.") (inputs `(("perl-array-utils" ,perl-array-utils) ("bioperl" ,bioperl-minimal) + ("perl-digest-md5-file" ,perl-digest-md5-file) ("perl-exception-class" ,perl-exception-class) ("perl-file-find-rule" ,perl-file-find-rule) ("perl-file-grep" ,perl-file-grep) @@ -5673,14 +5676,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "03hmbvp3i6lvd307fqdg7akxi2qp322rlky3bzw0zccgm0i0221g")))) + "0wlrp3v2jxw9is98ap39dfi7z97kmw1wv1xi4h7yfh12zpj2r8l0")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5700,14 +5703,14 @@ microarrays.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0a0ajns21db5rrjl16bq6wawggsnxr00fg184pc38nmfghv4z4b6")))) + "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -5725,14 +5728,14 @@ microarrays.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0sf2hdi9nv6r83vn1y65m4jiba8pffddpj46d6yjn5rlsixplmqg")))) + "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5752,14 +5755,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq")))) + "1hcxnkkjfvz4hj8iqidshwsjq7jnl1z7wj63dvcwlx1zx5aichyh")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5789,14 +5792,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg")))) + "0qxwnz2ffhav9slcn095k206cfza9i3i5l7w1154plf08gpy1d1d")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -5832,14 +5835,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx")))) + "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5862,14 +5865,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "11db6kvz453ypj9ds3xpjqzwrrjck84ijn4wlhkfyz2dzdgd5ryv")))) + "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) @@ -5883,14 +5886,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1c6i6g4fj3b8wjyxyygr7i3v8sxrq1ffb2bbicya5ah2gdaclfad")))) + "0kpkl6c5lrar6ip7wlhvd5axqlb9lb5l3lgbdb3dlih32c3nz0yq")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -5910,14 +5913,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn")))) + "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -5930,7 +5933,7 @@ Enrichment Analysis} (GSEA).") ("r-gseabase" ,r-gseabase) ("r-matrix" ,r-matrix) ("r-rbgl" ,r-rbgl) - ("r-rsqlite" ,r-rsqlite))) + ("r-dbi" ,r-dbi))) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -5941,14 +5944,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "0qvqjgfnd9ap4rikvyxa9p4dhcnccvkw8phzv88vghh6pq463d62")))) + "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -5959,6 +5962,7 @@ analysis.") ("r-category" ,r-category) ("r-go-db" ,r-go-db) ("r-graph" ,r-graph) + ("r-rgraphviz" ,r-rgraphviz) ("r-rbgl" ,r-rbgl))) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") @@ -5971,14 +5975,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0ayk3d5625ymb5g2gycq6banzqmyd642xrwjzhdshz2dwid7kly8")))) + "06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6013,14 +6017,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0c3m5rq63ypv15yca97yag5d4vgd7xj9by2a4sd8z0pcmpajz0hw")))) + "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -6059,14 +6063,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "16k1kp4sbhh0vp7dzywafq52csq42ksqfrqfy4bdv1qbd7536dpd")))) + "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -6141,7 +6145,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.5.2") + (version "2.6.0") (source (origin (method url-fetch) @@ -6151,7 +6155,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1z10psrwhflchwzw1fvzwnsn59xglf94qrn7msj93fpnjgafvmks")) + "0rplgpvsdkxw0k371ckxrp6i77jn93ckhslaazwbyd85m83nkynr")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -6378,13 +6382,13 @@ barplots or heatmaps.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0qbmz2qxwwi30xpxpvp2h1h7l494rbbz5d9pls5cfhqdv3wnpzsv")))) + "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -6398,13 +6402,13 @@ packages.") (define-public r-biocinstaller (package (name "r-biocinstaller") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocInstaller" version)) (sha256 (base32 - "0njw2q3lq1rrjx8qzw5d2130l72bmd3g2z8qlxqmkdcbmmgliyj2")))) + "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d")))) (properties `((upstream-name . "BiocInstaller"))) (build-system r-build-system) @@ -6417,13 +6421,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "17hi8w0w63f5yc43kid5pbld3ca78sj6n8x9dmkbl8h48818xbga")))) + "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -6433,7 +6437,6 @@ Bioconductor, CRAN, and Github.") ("r-rbgl" ,r-rbgl) ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml) - ("r-knitr" ,r-knitr) ("r-runit" ,r-runit))) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") @@ -6467,13 +6470,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.4.1") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c")))) + "05f2j9fx8s5gh4f8qkl6wcz32ghz04wxhqb3xxcn1bj24qd7x1x8")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -6492,13 +6495,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "01zkw5hggzvn0wj4msac71k1mknq4h2inn1c2hwqgw4cy1675wl0")))) + "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -6521,15 +6524,14 @@ functionality.") (symlink (string-append script-dir "/BiocCheck") (string-append dest-dir "/BiocCheck"))) #t))))) - (native-inputs - `(("which" ,which))) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-optparse" ,r-optparse) ("r-biocinstaller" ,r-biocinstaller) - ("r-biocviews" ,r-biocviews))) + ("r-biocviews" ,r-biocviews) + ("r-stringdist" ,r-stringdist))) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -6584,13 +6586,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.50.1") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p")))) + "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -6606,13 +6608,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.14.3") + (version "0.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs")))) + "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -6658,13 +6660,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.10.2") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy")))) + "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -6687,7 +6689,7 @@ possible.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "0.99.0") + (version "0.99.1") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -6697,7 +6699,7 @@ possible.") version ".tar.gz")) (sha256 (base32 - "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25")))) + "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -6710,13 +6712,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp")))) + "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6738,18 +6740,19 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.18.0") + (version "3.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "02l17i6xh33dv10swwvyfxrmv5kp23iv278iwvkfq2mnipasfnb9")))) + "01qnxwr9rmz8r5ga3hvjk632365ga2aygx71mxkk7jiad2pjznsp")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) ("r-statmod" ,r-statmod))) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") @@ -6765,13 +6768,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.22.3") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr")))) + "1lllp2vgyfbrar1yg28ji7am470hfzrzxm1bgdk68xpnrwcgcl25")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6803,13 +6806,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.32.5") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw")))) + "0a15gsaky0hfrkx8wrrmp0labzxpq6m2hrd33zl206wyas8bqzcs")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6822,13 +6825,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.16.0") + (version "0.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "01n09f4jdm60684lzikp02zf9gjan8bdrjx740vggr21q9fa69wn")))) + "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -6858,13 +6861,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.28.4") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z")))) + "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -6887,13 +6890,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.36.2") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f")))) + "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -6909,13 +6912,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj")))) + "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6936,19 +6939,21 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8")))) + "1dn3ysf0vb3mmg2b3380g0j1ajf88x4rh7fddfp990h2xlnsy2cx")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-progress" ,r-progress) ("r-rcurl" ,r-rcurl) + ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") @@ -6966,19 +6971,20 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0")))) + "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) (propagated-inputs `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow))) + ("r-snow" ,r-snow) + ("r-bh" ,r-bh))) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -6990,13 +6996,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.44.2") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp")))) + "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7016,13 +7022,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1zx6vhdz3lksbfy98jj3qzl7cxgspigm2pbsd5835b12r6mc5w6d")))) + "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7060,13 +7066,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.2.7") + (version "0.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) + "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7090,13 +7096,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) + "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7121,13 +7127,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "03ysxi9fdd3bcfj05iaysya9knn2aa2irwpypb5srg0xwv92bdb9")))) + "0sw30lj11wv7ifzypqm04lcah987crqwvj48wz3flaw3biw41zfi")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7154,13 +7160,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.36.4") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) + "12al1ygzy9p4myxa1fd817m28x2fj6f863znk9bw3hp7knbi98dh")))) (build-system r-build-system) (arguments `(#:phases @@ -7168,7 +7174,7 @@ alignments.") (add-after 'unpack 'use-system-zlib (lambda _ (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) + ((" zlibbioc,") "")) (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") "")) #t))))) @@ -7199,13 +7205,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.28.4") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) + "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7221,6 +7227,7 @@ as well as query and modify the browser state, such as the current viewport.") ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite) + ("r-rmysql" ,r-rmysql) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) @@ -7240,7 +7247,7 @@ extracting the desired features in a convenient format.") (define-public r-go-db (package (name "r-go-db") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) (uri (string-append "https://www.bioconductor.org/packages/" @@ -7248,7 +7255,7 @@ extracting the desired features in a convenient format.") version ".tar.gz")) (sha256 (base32 - "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl")))) + "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -7264,13 +7271,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-graph (package (name "r-graph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0hx9wslnrci7c5i1gd1zlpjmgrkdnx9gabfgmzzwfnykk1mdvvna")))) + "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -7283,13 +7290,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "04kvxz9qsxfz0np7wlrzp4r95nykz94x7mqpyyk76f90g6m66vcc")))) + "1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -7316,13 +7323,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "18dlknwk3xvi52hamxf9pl5bjc5806mpw98xwvx5xajn8mrxiy5h")))) + "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7377,13 +7384,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0va45vfixy3np549md87h3b3rbavm54gfnmnjhpr9hf02lll6zxs")))) + "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -7397,13 +7404,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0yw5251sirv3283xgmfmfbf900xp8dwvqfk88mr945s3by5hx99v")))) + "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -7424,13 +7431,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0r71nf8p3aq3yffqxg4yir1zmm7rar5a57nmy1kpqpn8kaf2svjl")))) + "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -7449,14 +7456,11 @@ reference point and sorted by a user defined feature.") ("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 @@ -7473,7 +7477,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.6.0") + (version "1.10.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7483,7 +7487,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y")))) + "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. @@ -7501,7 +7505,7 @@ downloaded from Encode.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7511,7 +7515,7 @@ downloaded from Encode.") "org.Hs.eg.db_" version ".tar.gz")) (sha256 (base32 - "19mg64pw8zcvb9yxzzyf7caz1kvdrkfsj1hd84bzq7crrh8kc4y6")))) + "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -7520,14 +7524,14 @@ downloaded from Encode.") (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description - "This package provides mappings from Entrez gene identifiers to various -annotations for the human genome.") + "This package contains genome-wide annotations for Human, primarily based +on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7537,7 +7541,7 @@ annotations for the human genome.") "org.Ce.eg.db_" version ".tar.gz")) (sha256 (base32 - "12llfzrrc09kj2wzbisdspv38qzkzgpsbn8kv7qkwg746k3pq436")))) + "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) @@ -7553,7 +7557,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7563,7 +7567,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") "org.Dm.eg.db_" version ".tar.gz")) (sha256 (base32 - "1vzbphbrh1cf7xi5cksia9xy9a9l42js2z2qsajvjxvddiphrb7j")))) + "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) @@ -7579,7 +7583,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7589,7 +7593,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") "org.Mm.eg.db_" version ".tar.gz")) (sha256 (base32 - "1lykjqjaf01fmgg3cvfcvwd5xjq6zc5vbxnm5r4l32fzvl89q50c")))) + "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) @@ -7605,14 +7609,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q")))) + "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -7851,20 +7855,20 @@ Biostrings objects.") (define-public r-motifrg (package (name "r-motifrg") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "0lxxpqyljiyk73vyq6ss46q13g81pm24q87mkzdsqlr5zx427ch6")))) + "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-iranges" ,r-iranges) ("r-seqlogo" ,r-seqlogo) ("r-xvector" ,r-xvector))) @@ -7903,13 +7907,13 @@ two-dimensional genome scans.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1kdgwwlh39mgwzj3zq71za4iv40sq625ghnyrndv5wrivrcr2igv")))) + "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -7945,14 +7949,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0jj5h81z5gyf4j3lp2l3zsm6pgbmalgrngr8qdpygc20phndpp0b")))) + "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs @@ -7972,14 +7976,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0knx69zzdaak2sjim8k9mygmcjxpa705m8013ld5zwpgi8dag9mc")))) + "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8094,14 +8098,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg")))) + "0sqbrswg8ylkjb9q3vqcb5ggwixynwj6hyv2n4sk7snyk61z3fq9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8117,6 +8121,9 @@ library implementing most of the pipeline's features.") ("r-plyr" ,r-plyr) ("r-pracma" ,r-pracma) ("r-reshape2" ,r-reshape2) + ("r-cowplot" ,r-cowplot) + ("r-ggdendro" ,r-ggdendro) + ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) (home-page "https://bioconductor.org/packages/MutationalPatterns/") @@ -8267,13 +8274,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (define-public r-tximport (package (name "r-tximport") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx")))) + "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8289,13 +8296,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1p6f5i6l44phl772a38x9cav2sya37bkqbkjzdc4pmyfzkv1j6hy")))) + "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1")))) (build-system r-build-system) (arguments `(#:phases @@ -8332,13 +8339,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7")))) + "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -8588,17 +8595,18 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "032svgym67k2ds7wp0cxzv79gi30yrdl45zbqn74lni3dk04qm33")))) + "0fx1sx53znbgzfhbbiyd8j6cg5llpcsl5q5c45jy2c81d12piqfd")))) (build-system python-build-system) (propagated-inputs - `(("python-jinja2" ,python-jinja2) + `(("python-enum34" ,python-enum34) + ("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) ("python-click" ,python-click) @@ -8616,24 +8624,25 @@ replacement for strverscmp.") "MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.") - (license license:gpl3))) + (license license:gpl3+))) (define-public r-chipseq (package (name "r-chipseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1hahyqiwb2ch8214xqpw0c3jpiwkmyf3dwz0xc87jx6cdnzipj3i")))) + "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread))) (home-page "https://bioconductor.org/packages/chipseq") @@ -8672,14 +8681,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) + "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -8712,13 +8721,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm")))) + "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -8742,7 +8751,7 @@ number detection tools.") ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) - (home-page "http://code.google.com/p/methylkit/") + (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") (description @@ -8758,14 +8767,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.24.4") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) + "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -8868,14 +8877,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "08idb3rvxn4fl7rd66jasyqz47cb76dbc3968r1g26jr2ci3w1pl")))) + "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -8888,18 +8897,35 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1zir46h320n2vbrky6q3m8l221f3wdjlfsnx4ak9xca5min24xm7")))) + "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) (properties `((upstream-name . "mzR"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + (("ARCH_OBJS=" line) + (string-append line + "\nARCH_LIBS=-lboost_system -lboost_regex \ +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) + #t))))) (inputs - `(("boost" ,boost) + `(("boost" ,boost) ; use this instead of the bundled boost sources ("netcdf" ,netcdf))) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -8921,14 +8947,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "13w6al9296q916w0w6ngbsk25b21ahla1b6n40fcqhbvhyfii6sj")))) + "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -8945,14 +8971,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0azwg2qxzgflr1rjvbdln5i5rbcr9gs36kqlacd9cwl1szb9ad3m")))) + "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -8971,20 +8997,19 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0qhg3a4sc62pfdxcpvmk831rk138xh4zx4f1s39jhxpqqhmr7jvk")))) + "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma))) (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") @@ -9006,14 +9031,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "11xnild02jz24vbsfy92lb7jlqqwnrswg66a7r4rsw8d2ibrbk33")))) + "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9036,14 +9061,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0c4lphqyzj577ws4s172391cgv00s5nhy152zp18k2k4diyhq6n0")))) + "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9066,14 +9091,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1n9bbdlp8d8bx2mqby0c4yylz1yil42scbkxqgyrfr9s5sn6dqff")))) + "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9085,6 +9110,7 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-ggplot2" ,r-ggplot2) ("r-impute" ,r-impute) ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) ("r-maldiquant" ,r-maldiquant) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) @@ -9093,7 +9119,6 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-preprocesscore" ,r-preprocesscore) ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) @@ -9107,14 +9132,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.10.0") + (version "1.11.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0pjwargi5lif8q53fd43ql67p3yk9w10jychafd9qgbaw5k3f68k")))) + "1vi4ngwbayrv2jkfb4pbmdp37xn04y07rh1jcklqfh0fcrm1jdig")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9225,14 +9250,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "10snykmmx36qaymyf5s1n1km8hsscyzpykcpf0mzsrcv8ml9rp8a")))) + "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9252,14 +9277,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0j3dgcxd64m9qknmlcbdzvg4xhp981xd6nbwsvnqjfn6yypslgyw")))) + "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9283,14 +9308,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a")))) + "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9321,14 +9346,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7")))) + "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -9345,20 +9370,21 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.8.2") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r")))) + "1arfka3czw8hkv6n2d85bgibq81s2rgkwhmpaxzhy6nw39vv7y8b")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biocinstaller" ,r-biocinstaller) + ("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-interactivedisplaybase" ,r-interactivedisplaybase) ("r-rsqlite" ,r-rsqlite) @@ -9379,14 +9405,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h")))) + "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9406,17 +9432,731 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-keggrest + (package + (name "r-keggrest") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGREST" version)) + (sha256 + (base32 + "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj")))) + (properties `((upstream-name . "KEGGREST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-httr" ,r-httr) + ("r-png" ,r-png))) + (home-page "https://bioconductor.org/packages/KEGGREST") + (synopsis "Client-side REST access to KEGG") + (description + "This package provides a package that provides a client interface to the +@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") + (license license:artistic2.0))) + +(define-public r-gage + (package + (name "r-gage") + (version "2.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page "http://www.biomedcentral.com/1471-2105/10/161") + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These funtions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n")))) + (properties `((upstream-name . "GenomicFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + +(define-public r-complexheatmap + (package + (name "r-complexheatmap") + (version "1.17.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ComplexHeatmap" version)) + (sha256 + (base32 + "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy")))) + (properties + `((upstream-name . "ComplexHeatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-colorspace" ,r-colorspace) + ("r-getoptlong" ,r-getoptlong) + ("r-globaloptions" ,r-globaloptions) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page + "https://github.com/jokergoo/ComplexHeatmap") + (synopsis "Making Complex Heatmaps") + (description + "Complex heatmaps are efficient to visualize associations between +different sources of data sets and reveal potential structures. This package +provides a highly flexible way to arrange multiple heatmaps and supports +self-defined annotation graphics.") + (license license:gpl2+))) + +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + +(define-public r-organismdbi + (package + (name "r-organismdbi") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OrganismDbi" version)) + (sha256 + (base32 + "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8")))) + (properties `((upstream-name . "OrganismDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocinstaller" ,r-biocinstaller) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-graph" ,r-graph) + ("r-iranges" ,r-iranges) + ("r-rbgl" ,r-rbgl) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/OrganismDbi") + (synopsis "Software to enable the smooth interfacing of database packages") + (description "The package enables a simple unified interface to several +annotation packages each of which has its own schema by taking advantage of +the fact that each of these packages implements a select methods.") + (license license:artistic2.0))) + +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f")))) + (properties `((upstream-name . "biovizBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dichromat" ,r-dichromat) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +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 "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) + (build-system r-build-system) + (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-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (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-gprofiler + (package + (name "r-gprofiler") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gProfileR" version)) + (sha256 + (base32 + "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p")))) + (properties `((upstream-name . "gProfileR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-plyr" ,r-plyr) + ("r-rcurl" ,r-rcurl))) + (home-page "http://cran.r-project.org/web/packages/gProfileR/") + (synopsis "Interface to the g:Profiler toolkit") + (description + "This package provides tools for functional enrichment analysis, +gene identifier conversion and mapping homologous genes across related +organisms via the @code{g:Profiler} toolkit.") + (license license:gpl2+))) + +(define-public r-gqtlbase + (package + (name "r-gqtlbase") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLBase" version)) + (sha256 + (base32 + "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035")))) + (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))) + (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 "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "snpStats" version)) + (sha256 + (base32 + "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir")))) + (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 "http://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 "0.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "erma" version)) + (sha256 + (base32 + "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-foreach" ,r-foreach) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (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 "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ldblock" version)) + (sha256 + (base32 + "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) + (build-system r-build-system) + (propagated-inputs + `(("r-erma" ,r-erma) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-go-db" ,r-go-db) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (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 "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLstats" version)) + (sha256 + (base32 + "1cbdqawxzgna8rrgj3siph5sw4d2pb57qc0gn6ibfkhyk45f8gdv")))) + (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-iranges" ,r-iranges) + ("r-ldblock" ,r-ldblock) + ("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))) + (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 "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Gviz" version)) + (sha256 + (base32 + "1lrw65a8426wpxw975wjcaiacpp6fqa00nif1yxigyankbfs23c8")))) + (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-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))) + (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 "2.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gwascat" version)) + (sha256 + (base32 + "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gqtlstats" ,r-gqtlstats) + ("r-graph" ,r-graph) + ("r-gviz" ,r-gviz) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-snpstats" ,r-snpstats) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (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 "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Sushi" version)) + (sha256 + (base32 + "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g")))) + (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-fithic + (package + (name "r-fithic") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "FitHiC" version)) + (sha256 + (base32 + "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n")))) + (properties `((upstream-name . 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"HiTC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "https://bioconductor.org/packages/HiTC") + (synopsis "High throughput chromosome conformation capture analysis") + (description + "The HiTC package was developed to explore high-throughput \"C\" data +such as 5C or Hi-C. Dedicated R classes as well as standard methods for +quality controls, normalization, visualization, and further analysis are also +provided.") + (license license:artistic2.0))) + (define-public r-qvalue (package (name "r-qvalue") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i")))) + "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) |