;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Roel Janssen ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages haskell) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) ;;; Annotations (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") (version "1.4.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Celegans.UCSC.ce6_" version ".tar.gz")) (sha256 (base32 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") (synopsis "Full genome sequences for Worm") (description "This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-celegans-ucsc-ce10 (package (name "r-bsgenome-celegans-ucsc-ce10") (version "1.4.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Celegans.UCSC.ce10_" version ".tar.gz")) (sha256 (base32 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") (synopsis "Full genome sequences for Worm") (description "This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-dmelanogaster-ucsc-dm6 (package (name "r-bsgenome-dmelanogaster-ucsc-dm6") (version "1.4.1") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Dmelanogaster.UCSC.dm6_" version ".tar.gz")) (sha256 (base32 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) (properties `((upstream-name . 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(uri (string-append "http://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Dmelanogaster.UCSC.dm3.masked_" version ".tar.gz")) (sha256 (base32 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) (properties `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3))) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") (synopsis "Full masked genome sequences for Fly") (description "This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") (version "0.99.1") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Hsapiens.1000genomes.hs37d5_" version ".tar.gz")) (sha256 (base32 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) (properties `((upstream-name . 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(uri (string-append "http://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Hsapiens.UCSC.hg19.masked_" version ".tar.gz")) (sha256 (base32 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19))) (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") (synopsis "Full masked genome sequences for Homo sapiens") (description "This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) (define-public r-bsgenome-mmusculus-ucsc-mm9 (package (name "r-bsgenome-mmusculus-ucsc-mm9") (version "1.4.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Mmusculus.UCSC.mm9_" version ".tar.gz")) (sha256 (base32 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) (properties `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") (synopsis "Full genome sequences for Mouse") (description "This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-mmusculus-ucsc-mm9-masked (package (name "r-bsgenome-mmusculus-ucsc-mm9-masked") (version "1.3.99") (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/" "BSgenome.Mmusculus.UCSC.mm9.masked_" version ".tar.gz")) (sha256 (base32 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) (properties `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9))) (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description "This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default." ) (license license:artistic2.0))) (define-public r-bsgenome-mmusculus-ucsc-mm10 (package (name "r-bsgenome-mmusculus-ucsc-mm10") (version "1.4.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "BSgenome.Mmusculus.UCSC.mm10_" version ".tar.gz")) (sha256 (base32 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) (properties `((upstream-name . 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(uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "org.Dm.eg.db_" version ".tar.gz")) (sha256 (base32 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description "This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.") (license license:artistic2.0))) (define-public r-org-dr-eg-db (package (name "r-org-dr-eg-db") (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "org.Dr.eg.db_" version ".tar.gz")) (sha256 (base32 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) (properties `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description "This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "org.Hs.eg.db_" version ".tar.gz")) (sha256 (base32 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description "This package contains genome-wide annotations for Human, primarily based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "org.Mm.eg.db_" version ".tar.gz")) (sha256 (base32 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description "This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus.") (license license:artistic2.0))) (define-public r-bsgenome-hsapiens-ucsc-hg19 (package (name "r-bsgenome-hsapiens-ucsc-hg19") (version "1.4.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". 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(license license:artistic2.0))) (define-public r-genelendatabase (package (name "r-genelendatabase") (version "1.18.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/experiment/" instead of "bioc/". (uri (string-append "https://bioconductor.org/packages/" "release/data/experiment/src/contrib" "/geneLenDataBase_" version ".tar.gz")) (sha256 (base32 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs `(("r-rtracklayer" ,r-rtracklayer) ("r-genomicfeatures" ,r-genomicfeatures))) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description "This package provides the lengths of mRNA transcripts for a number of genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) (define-public r-txdb-hsapiens-ucsc-hg19-knowngene (package (name "r-txdb-hsapiens-ucsc-hg19-knowngene") (version "3.2.2") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://bioconductor.org/packages/" "release/data/annotation/src/contrib" "/TxDb.Hsapiens.UCSC.hg19.knownGene_" version ".tar.gz")) (sha256 (base32 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. 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(uri (string-append "https://bioconductor.org/packages/" "release/data/annotation/src/contrib" "/TxDb.Mmusculus.UCSC.mm9.knownGene_" version ".tar.gz")) (sha256 (base32 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-annotationdbi" ,r-annotationdbi))) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") (description "This package provides an annotation database of Mouse genome data. It is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") (version "3.4.4") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "TxDb.Mmusculus.UCSC.mm10.knownGene_" version ".tar.gz")) (sha256 (base32 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-genomicfeatures" ,r-genomicfeatures) ("r-annotationdbi" ,r-annotationdbi))) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") (description "This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.") (license license:artistic2.0))) (define-public r-fdb-infiniummethylation-hg19 (package (name "r-fdb-infiniummethylation-hg19") (version "2.2.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "FDb.InfiniumMethylation.hg19_" version ".tar.gz")) (sha256 (base32 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) (properties `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-genomicfeatures" ,r-genomicfeatures) ("r-annotationdbi" ,r-annotationdbi) ("r-org-hs-eg-db" ,r-org-hs-eg-db) ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description "This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.") (license license:artistic2.0))) (define-public r-illuminahumanmethylationepicmanifest (package (name "r-illuminahumanmethylationepicmanifest") (version "0.3.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "IlluminaHumanMethylationEPICmanifest_" version ".tar.gz")) (sha256 (base32 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) (build-system r-build-system) (propagated-inputs `(("r-minfi" ,r-minfi))) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") (synopsis "Manifest for Illumina's EPIC methylation arrays") (description "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) (define-public r-do-db (package (name "r-do-db") (version "2.9") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "DO.db_" version ".tar.gz")) (sha256 (base32 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) (properties `((upstream-name . "DO.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/DO.db/") (synopsis "Annotation maps describing the entire Disease Ontology") (description "This package provides a set of annotation maps describing the entire Disease Ontology.") (license license:artistic2.0))) ;;; Experiment data (define-public r-abadata (package (name "r-abadata") (version "1.12.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/experiment/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/experiment/src/contrib/" "ABAData_" version ".tar.gz")) (sha256 (base32 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) (properties `((upstream-name . "ABAData"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/ABAData/") (synopsis "Gene expression in human brain regions from Allen Brain Atlas") (description "This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas: @enumerate @item Gene expression data from Human Brain (adults) averaged across donors, @item Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors, and @item a developmental effect score based on the Developing Human Brain expression data. @end enumerate All datasets are restricted to protein coding genes.") (license license:gpl2+))) (define-public r-arrmdata (package (name "r-arrmdata") (version "1.18.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/experiment/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/experiment/src/contrib/" "ARRmData_" version ".tar.gz")) (sha256 (base32 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) (home-page "https://www.bioconductor.org/packages/ARRmData/") (synopsis "Example dataset for normalization of Illumina 450k methylation data") (description "This package provides raw beta values from 36 samples across 3 groups from Illumina 450k methylation arrays.") (license license:artistic2.0))) (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") (version "1.2.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/experiment/" instead of "bioc/". (uri (string-append "https://www.bioconductor.org/packages/" "release/data/experiment/src/contrib/" "HSMMSingleCell_" version ".tar.gz")) (sha256 (base32 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") (description "Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) ;;; Packages (define-public r-biocgenerics (package (name "r-biocgenerics") (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocGenerics") (synopsis "S4 generic functions for Bioconductor") (description "This package provides S4 generic functions needed by many Bioconductor packages.") (license license:artistic2.0))) (define-public r-annotate (package (name "r-annotate") (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml) ("r-xtable" ,r-xtable))) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") (description "This package provides R environments for the annotation of microarrays.") (license license:artistic2.0))) (define-public r-hpar (package (name "r-hpar") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from the Human Protein Atlas project.") (license license:artistic2.0))) (define-public r-regioner (package (name "r-regioner") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-memoise" ,r-memoise) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) (define-public r-geneplotter (package (name "r-geneplotter") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-lattice" ,r-lattice) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description "This package provides functions for plotting genomic data.") (license license:artistic2.0))) (define-public r-qvalue (package (name "r-qvalue") (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) (home-page "http://github.com/jdstorey/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local @dfn{false discovery rate} (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-diffbind (package (name "r-diffbind") (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-amap" ,r-amap) ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-rcolorbrewer" , r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper) ("r-zlibbioc" ,r-zlibbioc))) (home-page "http://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description "This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.") (license license:artistic2.0))) (define-public r-ripseeker (package (name "r-ripseeker") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rsamtools" ,r-rsamtools) ("r-genomicalignments" ,r-genomicalignments) ("r-rtracklayer" ,r-rtracklayer))) (home-page "http://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") (description "This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) (define-public r-multtest (package (name "r-multtest") (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) ("r-biocgenerics" ,r-biocgenerics) ("r-biobase" ,r-biobase) ("r-mass" ,r-mass))) (home-page "http://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description "This package can do non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of T- and F-statistics (including T-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with T-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted P-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) (define-public r-graph (package (name "r-graph") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) (define-public r-codedepends (package (name "r-codedepends") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "CodeDepends" version)) (sha256 (base32 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) (properties `((upstream-name . 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There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-chippeakanno (package (name "r-chippeakanno") (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-go-db" ,r-go-db) ("r-biomart" ,r-biomart) ("r-bsgenome" ,r-bsgenome) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-genomeinfodb" ,r-genomeinfodb) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-annotationdbi" ,r-annotationdbi) ("r-limma" ,r-limma) ("r-multtest" ,r-multtest) ("r-rbgl" ,r-rbgl) ("r-graph" ,r-graph) ("r-regioner" ,r-regioner) ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) ("r-biobase" ,r-biobase) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-idr" ,r-idr) ("r-genomicalignments" ,r-genomicalignments) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rsamtools" ,r-rsamtools) ("r-venndiagram" ,r-venndiagram))) (home-page "http://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description "The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).") (license license:gpl2+))) (define-public r-marray (package (name "r-marray") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted microarray data. It also includes fuctions for data input, diagnostic plots, normalization and quality checking.") (license license:lgpl2.0+))) (define-public r-cghbase (package (name "r-cghbase") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-marray" ,r-marray))) (home-page "http://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by the @code{arrayCGH} packages.") (license license:gpl2+))) (define-public r-cghcall (package (name "r-cghcall") (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-bayseq (package (name "r-bayseq") (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-edger" ,r-edger) ("r-genomicranges" ,r-genomicranges))) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description "This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.") (license license:gpl3))) (define-public r-chipcomp (package (name "r-chipcomp") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description "ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-riboprofiling (package (name "r-riboprofiling") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-riboseqr (package (name "r-riboseqr") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-bayseq" ,r-bayseq) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-seqlogo" ,r-seqlogo))) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description "This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) (define-public r-interactionset (package (name "r-interactionset") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description "This packages provides the @code{GInteractions}, @code{InteractionSet} and @code{ContactMatrix} objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.") (license license:gpl3))) (define-public r-genomicinteractions (package (name "r-genomicinteractions") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) (properties `((upstream-name . 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(license license:lgpl2.0+))) (define-public r-glimma (package (name "r-glimma") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) ("r-jsonlite" ,r-jsonlite) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description "This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.") (license license:lgpl3))) (define-public r-rots (package (name "r-rots") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description "This package provides tools for calculating the @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing in omics data.") 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(license license:gpl2))) (define-public r-inspect (package (name "r-inspect") (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 "1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-dnabarcodes (package (name "r-dnabarcodes") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description "This package offers tools to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.") (license license:gpl2))) (define-public r-ruvseq (package (name "r-ruvseq") (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-edaseq" ,r-edaseq) ("r-edger" ,r-edger) ("r-mass" ,r-mass))) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description "This package implements methods to @dfn{remove unwanted variation} (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.") (license license:artistic2.0))) (define-public r-biocneighbors (package (name "r-biocneighbors") (version "1.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-rcpp" ,r-rcpp) ("r-rcppannoy" ,r-rcppannoy) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description "This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) (define-public r-destiny (package (name "r-destiny") (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-fnn" ,r-fnn) ("r-ggthemes" ,r-ggthemes) ("r-hmisc" ,r-hmisc) ("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-vim" ,r-vim))) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-savr (package (name "r-savr") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-copynumber (package (name "r-copynumber") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description "This package segments single- and multi-track copy number data by a penalized least squares regression method.") (license license:artistic2.0))) (define-public r-dnacopy (package (name "r-dnacopy") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://bioconductor.org/packages/DNAcopy") (synopsis "DNA copy number data analysis") (description "This package implements the @dfn{circular binary segmentation} (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.") (license license:gpl2+))) ;; This is a CRAN package, but it uncharacteristically depends on a ;; Bioconductor package. (define-public r-htscluster (package (name "r-htscluster") (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "HTSCluster" version)) (sha256 (base32 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) (properties `((upstream-name . 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"DEDS"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DEDS/") (synopsis "Differential expression via distance summary for microarray data") (description "This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.") ;; Any version of the LGPL. (license license:lgpl3+))) ;; This is a CRAN package, but since it depends on a Bioconductor package we ;; put it here. 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The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code, while Rsymphony expects to find header and library files on the users' system. Thus the intention of @code{lpsymphony} is to provide an easy to install interface to SYMPHONY.") ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. ;; lpsimphony is released under the same terms. (license license:epl1.0))) (define-public r-ihw (package (name "r-ihw") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-scone (package (name "r-scone") (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) ("r-biocparallel" ,r-biocparallel) ("r-boot" ,r-boot) ("r-class" ,r-class) ("r-cluster" ,r-cluster) ("r-compositions" ,r-compositions) ("r-diptest" ,r-diptest) ("r-edger" ,r-edger) ("r-fpc" ,r-fpc) ("r-gplots" ,r-gplots) ("r-hexbin" ,r-hexbin) ("r-limma" ,r-limma) ("r-matrixstats" ,r-matrixstats) ("r-mixtools" ,r-mixtools) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rhdf5" ,r-rhdf5) ("r-ruvseq" ,r-ruvseq) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description "SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.") 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(license license:gpl2))) (define-public r-illuminaio (package (name "r-illuminaio") (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description "This package provides tools for parsing Illumina's microarray output files, including IDAT.") 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(license license:lgpl2.0+))) (define-public r-bumphunter (package (name "r-bumphunter") (version "1.24.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-dorng" ,r-dorng) ("r-foreach" ,r-foreach) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-iterators" ,r-iterators) ("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description "This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) (define-public r-minfi (package (name "r-minfi") (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bumphunter" ,r-bumphunter) ("r-data-table" ,r-data-table) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-geoquery" ,r-geoquery) ("r-hdf5array" ,r-hdf5array) ("r-illuminaio" ,r-illuminaio) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-mass" ,r-mass) ("r-mclust" ,r-mclust) ("r-nlme" ,r-nlme) ("r-nor1mix" ,r-nor1mix) ("r-preprocesscore" ,r-preprocesscore) ("r-quadprog" ,r-quadprog) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-s4vectors" ,r-s4vectors) ("r-siggenes" ,r-siggenes) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description "This package provides tools to analyze and visualize Illumina Infinium methylation arrays.") (license license:artistic2.0))) (define-public r-methylumi (package (name "r-methylumi") (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-illuminaio" ,r-illuminaio) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-matrixstats" ,r-matrixstats) ("r-minfi" ,r-minfi) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description "This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) (define-public r-lumi (package (name "r-lumi") (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-dbi" ,r-dbi) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-kernsmooth" ,r-kernsmooth) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-methylumi" ,r-methylumi) ("r-mgcv" ,r-mgcv) ("r-nleqslv" ,r-nleqslv) ("r-preprocesscore" ,r-preprocesscore) ("r-rsqlite" ,r-rsqlite))) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.") (license license:lgpl2.0+))) (define-public r-linnorm (package (name "r-linnorm") (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6")))) (properties `((upstream-name . 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In addition to the transformtion function (@code{Linnorm}), the following pipelines are implemented: @enumerate @item Library size/batch effect normalization (@code{Linnorm.Norm}) @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or hierarchical clustering (@code{Linnorm.tSNE}, @code{Linnorm.PCA}, @code{Linnorm.HClust}) @item Differential expression analysis or differential peak detection using limma (@code{Linnorm.limma}) @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) @item Stable gene selection for scRNA-seq data; for users without or who do not want to rely on spike-in genes (@code{Linnorm.SGenes}) @item Data imputation (@code{Linnorm.DataImput}). @end enumerate Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the @code{RnaXSim} function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.") (license license:expat))) (define-public r-ioniser (package (name "r-ioniser") (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00")))) (properties `((upstream-name . 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(license license:expat))) ;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-gkmsvm (package (name "r-gkmsvm") (version "0.79.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-kernlab" ,r-kernlab) ("r-rcpp" ,r-rcpp) ("r-rocr" ,r-rocr) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr))) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description "This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) (define-public r-triform (package (name "r-triform") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-iranges" ,r-iranges) ("r-yaml" ,r-yaml))) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description "The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.") (license license:gpl2))) (define-public r-varianttools (package (name "r-varianttools") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j")))) (properties `((upstream-name . 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GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests: @enumerate @item the Wilcoxon rank-sum test that is used when genes are ranked, @item a binomial test that is used when genes are associated with two counts, and @item a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. @end enumerate To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.") (license license:gpl2+))) (define-public r-abaenrichment (package (name "r-abaenrichment") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs `(("r-abadata" ,r-abadata) ("r-data-table" ,r-data-table) ("r-gofuncr" ,r-gofuncr) ("r-gplots" ,r-gplots) ("r-gtools" ,r-gtools) ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description "The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function @code{aba_enrich} integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.") (license license:gpl2+))) (define-public r-annotationfuncs (package (name "r-annotationfuncs") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dbi" ,r-dbi))) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description "This package provides functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. @code{org.Bt.eg.db}).") (license license:gpl2))) (define-public r-annotationtools (package (name "r-annotationtools") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description "This package provides functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).") ;; Any version of the GPL. (license (list license:gpl2+)))) (define-public r-allelicimbalance (package (name "r-allelicimbalance") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-gridextra" ,r-gridextra) ("r-gviz" ,r-gviz) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-nlme" ,r-nlme) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description "This package provides a framework for allele-specific expression investigation using RNA-seq data.") (license license:gpl3))) (define-public r-aucell (package (name "r-aucell") (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description "AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area Under the Curve} (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.") (license license:gpl3))) (define-public r-ebimage (package (name "r-ebimage") (version "4.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-biocgenerics" ,r-biocgenerics) ("r-fftwtools" ,r-fftwtools) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jpeg" ,r-jpeg) ("r-locfit" ,r-locfit) ("r-png" ,r-png) ("r-rcurl" ,r-rcurl) ("r-tiff" ,r-tiff))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description "EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.") ;; Any version of the LGPL. (license license:lgpl2.1+))) (define-public r-yamss (package (name "r-yamss") (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-ebimage" ,r-ebimage) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-mzr" ,r-mzr) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description "This package provides tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.") (license license:artistic2.0))) (define-public r-gtrellis (package (name "r-gtrellis") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges))) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description "Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.") (license license:expat))) (define-public r-somaticsignatures (package (name "r-somaticsignatures") (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggbio" ,r-ggbio) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-nmf" ,r-nmf) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description "This package identifies mutational signatures of @dfn{single nucleotide variants} (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.") (license license:expat))) (define-public r-yapsa (package (name "r-yapsa") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-corrplot" ,r-corrplot) ("r-dendextend" ,r-dendextend) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) ("r-lsei" ,r-lsei) ("r-pmcmr" ,r-pmcmr) ("r-reshape2" ,r-reshape2) ("r-somaticsignatures" ,r-somaticsignatures) ("r-variantannotation" ,r-variantannotation))) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description "This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures and a signature analysis on @dfn{stratified mutational catalogue} (SMC) are provided.") (license license:gpl3))) (define-public r-gcrma (package (name "r-gcrma") (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-affyio" ,r-affyio) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-xvector" ,r-xvector))) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description "Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and @dfn{non-specific binding} (NSB). The main function @code{gcrma} converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific bidning is expected.") ;; Any version of the LGPL (license license:lgpl2.1+))) (define-public r-simpleaffy (package (name "r-simpleaffy") (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-gcrma" ,r-gcrma) ("r-genefilter" ,r-genefilter))) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description "This package provides high level functions for reading Affy @file{.CEL} files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the @code{affy} library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.") (license license:gpl2+))) (define-public r-yaqcaffy (package (name "r-yaqcaffy") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description "This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.") (license license:artistic2.0))) (define-public r-quantro (package (name "r-quantro") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-minfi" ,r-minfi) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description "This package provides a data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.") (license license:gpl3+))) (define-public r-yarn (package (name "r-yarn") (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biomart" ,r-biomart) ("r-downloader" ,r-downloader) ("r-edger" ,r-edger) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore) ("r-quantro" ,r-quantro) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-readr" ,r-readr))) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description "Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.") (license license:artistic2.0))) (define-public r-roar (package (name "r-roar") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description "This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.") (license license:gpl3))) (define-public r-xbseq (package (name "r-xbseq") (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-locfit" ,r-locfit) ("r-magrittr" ,r-magrittr) ("r-matrixstats" ,r-matrixstats) ("r-pracma" ,r-pracma) ("r-roar" ,r-roar))) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential expression} (DE), where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measurable observed signal and background noise from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.") (license license:gpl3+))) (define-public r-massspecwavelet (package (name "r-massspecwavelet") (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (propagated-inputs `(("r-waveslim" ,r-waveslim))) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) data mainly through the use of wavelet transforms. It supports peak detection based on @dfn{Continuous Wavelet Transform} (CWT).") (license license:lgpl2.0+))) (define-public r-xcms (package (name "r-xcms") (version "3.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) ("r-multtest" ,r-multtest) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-robustbase" ,r-robustbase) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description "This package provides a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. It imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.") (license license:gpl2+))) (define-public r-wrench (package (name "r-wrench") (version "1.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats))) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description "Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.") (license license:artistic2.0))) (define-public r-wiggleplotr (package (name "r-wiggleplotr") (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-cowplot" ,r-cowplot) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-purrr" ,r-purrr) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description "This package provides tools to visualize read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of exonic read coverage.") (license license:asl2.0))) (define-public r-widgettools (package (name "r-widgettools") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") (synopsis "Tools for creating interactive tcltk widgets") (description "This packages contains tools to support the construction of tcltk widgets in R.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-webbioc (package (name "r-webbioc") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) ("perl" ,perl))) (propagated-inputs `(("r-affy" ,r-affy) ("r-annaffy" ,r-annaffy) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-gcrma" ,r-gcrma) ("r-multtest" ,r-multtest) ("r-qvalue" ,r-qvalue) ("r-vsn" ,r-vsn))) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description "This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) (define-public r-zfpkm (package (name "r-zfpkm") (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description "This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).") (license license:gpl3))) (define-public r-rbowtie2 (package (name "r-rbowtie2") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description "This package provides an R wrapper of the popular @code{bowtie2} sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for rapid adapter trimming, identification, and read merging.") (license license:gpl3+))) (define-public r-progeny (package (name "r-progeny") (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description "This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication \"Perturbation-response genes reveal signaling footprints in cancer gene expression\".") (license license:asl2.0))) (define-public r-arrmnormalization (package (name "r-arrmnormalization") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description "This is a package to perform the @dfn{Adaptive Robust Regression method} (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.") (license license:artistic2.0)))