;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; 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 git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) #: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 graphviz) #:use-module (gnu packages haskell-xyz) #: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) #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) (properties `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description "This package provides genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers. Entrez Gene is National Center for Biotechnology Information (NCBI)’s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.") (license license:artistic2.0))) (define-public r-reactome-db (package (name "r-reactome-db") (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "reactome.db" version 'annotation)) (sha256 (base32 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://bioconductor.org/packages/reactome.db/") (synopsis "Annotation maps for reactome") (description "This package provides a set of annotation maps for the REACTOME database, assembled using data from REACTOME.") (license license:cc-by4.0))) (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" version 'annotation)) (sha256 (base32 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) (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) (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" version 'annotation)) (sha256 (base32 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) (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) (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" version 'annotation)) (sha256 (base32 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) (properties `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") (synopsis "Full genome sequences for Fly") (description "This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-dmelanogaster-ucsc-dm3 (package (name "r-bsgenome-dmelanogaster-ucsc-dm3") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" version 'annotation)) (sha256 (base32 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) (properties `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") (synopsis "Full genome sequences for Fly") (description "This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked (package (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") (version "1.3.99") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" version 'annotation)) (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) (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" version 'annotation)) (sha256 (base32 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) (properties `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") (synopsis "Full genome sequences for Homo sapiens") (description "This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") (license license:artistic2.0))) (define-public r-bsgenome-hsapiens-ncbi-grch38 (package (name "r-bsgenome-hsapiens-ncbi-grch38") (version "1.3.1000") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" version 'annotation)) (sha256 (base32 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://bioconductor.org/packages/release/data/annotation/html/\ BSgenome.Hsapiens.NCBI.GRCh38.html") (synopsis "Full genome sequences for Homo sapiens (GRCh38)") (description "This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-hsapiens-ucsc-hg19-masked (package (name "r-bsgenome-hsapiens-ucsc-hg19-masked") (version "1.3.99") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" version 'annotation)) (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) (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" version 'annotation)) (sha256 (base32 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) (properties `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) (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) (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" version 'annotation)) (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 "https://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) (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" version 'annotation)) (sha256 (base32 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) (properties `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") (synopsis "Full genome sequences for Mouse") (description "This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") (version "3.7.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) (sha256 (base32 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description "This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.") (license license:artistic2.0))) (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") (version "3.7.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) (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) (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) (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) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (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) (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) (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) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" version 'annotation)) (sha256 (base32 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") (synopsis "Full genome sequences for Homo sapiens") (description "This package provides full genome sequences for Homo sapiens as provided by UCSC (hg19, February 2009) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-bsgenome-hsapiens-ucsc-hg38 (package (name "r-bsgenome-hsapiens-ucsc-hg38") (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" version 'annotation)) (sha256 (base32 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") (description "This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-ensdb-hsapiens-v75 (package (name "r-ensdb-hsapiens-v75") (version "2.99.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) (sha256 (base32 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) (properties `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs `(("r-ensembldb" ,r-ensembldb))) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description "This package exposes an annotation database generated from Ensembl.") (license license:artistic2.0))) (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) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" version 'annotation)) (sha256 (base32 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures))) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") (description "This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") (version "3.4.6") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 (base32 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures))) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") (description "This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg38 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-mm9-knowngene (package (name "r-txdb-mmusculus-ucsc-mm9-knowngene") (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" version 'annotation)) (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 "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" version 'annotation)) (sha256 (base32 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (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-txdb-celegans-ucsc-ce6-ensgene (package (name "r-txdb-celegans-ucsc-ce6-ensgene") (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" version 'annotation)) (sha256 (base32 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) (properties `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-genomicfeatures" ,r-genomicfeatures))) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description "This package exposes a C elegans annotation database generated from UCSC by exposing these as TxDb objects.") (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) (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" version 'annotation)) (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) (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" version 'annotation)) (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-ideoviz (package (name "r-ideoviz") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb))) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs (package (name "r-deconstructsigs") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "deconstructSigs" version)) (sha256 (base32 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) (properties `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomeinfodb" ,r-genomeinfodb) ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package (name "r-nmf") (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-bigmemory" ,r-bigmemory) ; suggested ("r-synchronicity" ,r-synchronicity) ; suggested ("r-colorspace" ,r-colorspace) ("r-digest" ,r-digest) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gridbase" ,r-gridbase) ("r-pkgmaker" ,r-pkgmaker) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-registry" ,r-registry) ("r-reshape2" ,r-reshape2) ("r-rngtools" ,r-rngtools) ("r-stringr" ,r-stringr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description "This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) (define-public r-do-db (package (name "r-do-db") (version "2.9") (source (origin (method url-fetch) (uri (bioconductor-uri "DO.db" version 'annotation)) (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))) (define-public r-pasilla (package (name "r-pasilla") (version "1.14.0") (source (origin (method url-fetch) (uri (string-append "http://bioconductor.org/packages/release/data/experiment" "/src/contrib/pasilla_" version ".tar.gz")) (sha256 (base32 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) (build-system r-build-system) (propagated-inputs `(("r-biocstyle" ,r-biocstyle) ("r-dexseq" ,r-dexseq) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown))) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article 'Conservation of an RNA regulatory map between Drosophila and mammals' by Brooks et al., Genome Research 2011.") (license license:lgpl2.1+))) (define-public r-pfam-db (package (name "r-pfam-db") (version "3.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 (base32 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi))) (home-page "https://bioconductor.org/packages/PFAM.db") (synopsis "Set of protein ID mappings for PFAM") (description "This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories.") (license license:artistic2.0))) (define-public r-phastcons100way-ucsc-hg19 (package (name "r-phastcons100way-ucsc-hg19") (version "3.7.2") (source (origin (method url-fetch) (uri (bioconductor-uri "phastCons100way.UCSC.hg19" version 'annotation)) (sha256 (base32 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) (properties `((upstream-name . "phastCons100way.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-genomicscores" ,r-genomicscores) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") (synopsis "UCSC phastCons conservation scores for hg19") (description "This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.") (license license:artistic2.0))) ;;; Experiment data (define-public r-abadata (package (name "r-abadata") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAData" version 'experiment)) (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) (uri (bioconductor-uri "ARRmData" version 'experiment)) (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-genelendatabase (package (name "r-genelendatabase") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (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-hsmmsinglecell (package (name "r-hsmmsinglecell") (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) (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))) (define-public r-all (package (name "r-all") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 (base32 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description "The data consist of microarrays from 128 different individuals with @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates are available. The data have been normalized (using rma) and it is the jointly normalized data that are available here. The data are presented in the form of an @code{exprSet} object.") (license license:artistic2.0))) (define-public r-affydata (package (name "r-affydata") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 (base32 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy))) (home-page "https://bioconductor.org/packages/affydata/") (synopsis "Affymetrix data for demonstration purposes") (description "This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) (define-public r-gagedata (package (name "r-gagedata") (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") (synopsis "Auxillary data for gage package") (description "This is a supportive data package for the software package @code{gage}. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.") (license license:gpl2+))) (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 (base32 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) (propagated-inputs `(("r-annotationhub" ,r-annotationhub) ("r-experimenthub" ,r-experimenthub) ("r-hdf5array" ,r-hdf5array) ("r-multiassayexperiment" ,r-multiassayexperiment) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description "This package provides publicly available data from The Cancer Genome Atlas (TCGA) as @code{MultiAssayExperiment} objects. @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.") (license license:artistic2.0))) ;;; Packages (define-public r-biocversion (package (name "r-biocversion") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") (synopsis "Set the appropriate version of Bioconductor packages") (description "This package provides repository information for the appropriate version of Bioconductor.") (license license:artistic2.0))) (define-public r-biocgenerics (package (name "r-biocgenerics") (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) (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-coverageview (package (name "r-coverageview") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-genomicalignments" ,r-genomicalignments) ("r-rtracklayer" ,r-rtracklayer) ("r-rsamtools" ,r-rsamtools))) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome.") (license license:artistic2.0))) (define-public r-cummerbund (package (name "r-cummerbund") (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-fastcluster" ,r-fastcluster) ("r-ggplot2" ,r-ggplot2) ("r-gviz" ,r-gviz) ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/cummeRbund/") (synopsis "Analyze Cufflinks high-throughput sequencing data") (description "This package allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) (define-public r-bluster (package (name "r-bluster") (version "1.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs `(("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.") (license license:gpl3))) (define-public r-affycomp (package (name "r-affycomp") (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/affycomp/") (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") (description "The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.") (license license:gpl2+))) (define-public r-affycompatible (package (name "r-affycompatible") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/AffyCompatible/") (synopsis "Work with Affymetrix GeneChip files") (description "This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip Command Console} (AGCC)-compatible sample annotation files.") (license license:artistic2.0))) (define-public r-affycontam (package (name "r-affycontam") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-affydata" ,r-affydata) ("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/affyContam/") (synopsis "Structured corruption of Affymetrix CEL file data") (description "Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics.") (license license:artistic2.0))) (define-public r-affycoretools (package (name "r-affycoretools") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-edger" ,r-edger) ("r-gcrma" ,r-gcrma) ("r-glimma" ,r-glimma) ("r-ggplot2" ,r-ggplot2) ("r-gostats" ,r-gostats) ("r-gplots" ,r-gplots) ("r-hwriter" ,r-hwriter) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-oligoclasses" ,r-oligoclasses) ("r-reportingtools" ,r-reportingtools) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xtable" ,r-xtable))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description "This package provides various wrapper functions that have been written to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) (define-public r-affxparser (package (name "r-affxparser") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") (synopsis "Affymetrix File Parsing SDK") (description "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading @dfn{chip definition file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.") ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is ;; under LGPLv2+. (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) (define-public r-annotate (package (name "r-annotate") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-httr" ,r-httr) ("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 "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from the Human Protein Atlas project.") (license license:artistic2.0))) (define-public r-regioner (package (name "r-regioner") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) (define-public r-reportingtools (package (name "r-reportingtools") (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-category" ,r-category) ("r-deseq2" ,r-deseq2) ("r-edger" ,r-edger) ("r-ggbio" ,r-ggbio) ("r-ggplot2" ,r-ggplot2) ("r-gostats" ,r-gostats) ("r-gseabase" ,r-gseabase) ("r-hwriter" ,r-hwriter) ("r-iranges" ,r-iranges) ("r-knitr" ,r-knitr) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-pfam-db" ,r-pfam-db) ("r-r-utils" ,r-r-utils) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description "The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) (define-public r-geneplotter (package (name "r-geneplotter") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) (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-oligoclasses (package (name "r-oligoclasses") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-dbi" ,r-dbi) ("r-ff" ,r-ff) ("r-foreach" ,r-foreach) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description "This package contains class definitions, validity checks, and initialization methods for classes used by the @code{oligo} and @code{crlmm} packages.") (license license:gpl2+))) (define-public r-oligo (package (name "r-oligo") (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-affxparser" ,r-affxparser) ("r-affyio" ,r-affyio) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-dbi" ,r-dbi) ("r-ff" ,r-ff) ("r-oligoclasses" ,r-oligoclasses) ("r-preprocesscore" ,r-preprocesscore) ("r-rsqlite" ,r-rsqlite) ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description "This package provides a package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (license license:lgpl2.0+))) (define-public r-qvalue (package (name "r-qvalue") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/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 r-rcppnumerical (package (name "r-rcppnumerical") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (properties `((upstream-name . "RcppNumerical"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis "Rcpp integration for numerical computing libraries") (description "This package provides a collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-apeglm (package (name "r-apeglm") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs `(("r-emdbook" ,r-emdbook) ("r-genomicranges" ,r-genomicranges) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppnumerical" ,r-rcppnumerical) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.") (license license:gpl2))) (define-public r-greylistchip (package (name "r-greylistchip") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-mass" ,r-mass) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling.") (license license:artistic2.0))) (define-public r-diffbind (package (name "r-diffbind") (version "3.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap) ("r-apeglm" ,r-apeglm) ("r-ashr" ,r-ashr) ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) ("r-greylistchip" ,r-greylistchip) ("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-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper))) (home-page "https://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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (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 "https://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 "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) (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 "https://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 "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) (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))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-ggm (package (name "r-ggm") (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "ggm" version)) (sha256 (base32 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-igraph" ,r-igraph))) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description "This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. (define-public r-perfmeas (package (name "r-perfmeas") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "PerfMeas" version)) (sha256 (base32 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-limma" ,r-limma) ("r-rbgl" ,r-rbgl))) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description "This package implements different performance measures for classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package. (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 . "CodeDepends"))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) ("r-xml" ,r-xml))) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description "This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. 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 "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) ("r-iranges" ,r-iranges) ("r-keggrest" ,r-keggrest) ("r-matrixstats" ,r-matrixstats) ("r-multtest" ,r-multtest) ("r-rbgl" ,r-rbgl) ("r-regioner" ,r-regioner) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description "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-matrixgenerics (package (name "r-matrixgenerics") (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs `(("r-matrixstats" ,r-matrixstats))) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description "This package provides S4 generic functions modeled after the @code{matrixStats} API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.") (license license:artistic2.0))) (define-public r-marray (package (name "r-marray") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) (home-page "https://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 functions for data input, diagnostic plots, normalization and quality checking.") (license license:lgpl2.0+))) (define-public r-cghbase (package (name "r-cghbase") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-marray" ,r-marray))) (home-page "https://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 "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-cghbase" ,r-cghbase) ("r-impute" ,r-impute) ("r-dnacopy" ,r-dnacopy) ("r-snowfall" ,r-snowfall))) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @code{arrayCGH} packages.") (license license:gpl2+))) (define-public r-qdnaseq (package (name "r-qdnaseq") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-r-utils" ,r-r-utils) ("r-rsamtools" ,r-rsamtools))) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.") (license license:gpl2+))) (define-public r-bayseq (package (name "r-bayseq") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) (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 "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) (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 "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-data-table" ,r-data-table) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggbio" ,r-ggbio) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-sqldf" ,r-sqldf))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.") (license license:gpl3))) (define-public r-riboseqr (package (name "r-riboseqr") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) (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 ;BROKEN (name "r-interactionset") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description "This package 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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gviz" ,r-gviz) ("r-igraph" ,r-igraph) ("r-interactionset" ,r-interactionset) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description "This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics.") (license license:gpl3))) (define-public r-ctc (package (name "r-ctc") (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") (synopsis "Cluster and tree conversion") (description "This package provides tools for exporting and importing classification trees and clusters to other programs.") (license license:gpl2))) (define-public r-goseq (package (name "r-goseq") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biasedurn" ,r-biasedurn) ("r-biocgenerics" ,r-biocgenerics) ("r-genelendatabase" ,r-genelendatabase) ("r-go-db" ,r-go-db) ("r-mgcv" ,r-mgcv))) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description "This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.") (license license:lgpl2.0+))) (define-public r-glimma (package (name "r-glimma") (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs `(("r-deseq2" ,r-deseq2) ("r-edger" ,r-edger) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-limma" ,r-limma) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) (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.") (license license:gpl2+))) (define-public r-plgem (package (name "r-plgem") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-mass" ,r-mass))) (home-page "http://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description "The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.") (license license:gpl2))) (define-public r-inspect (package (name "r-inspect") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-desolve" ,r-desolve) ("r-gdata" ,r-gdata) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-kernsmooth" ,r-kernsmooth) ("r-plgem" ,r-plgem) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-txdb-mmusculus-ucsc-mm9-knowngene" ,r-txdb-mmusculus-ucsc-mm9-knowngene))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description "INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.") (license license:gpl2))) (define-public r-dnabarcodes (package (name "r-dnabarcodes") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description "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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcpphnsw" ,r-rcpphnsw) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description "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-biocsingular (package (name "r-biocsingular") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-irlba" ,r-irlba) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rsvd" ,r-rsvd) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description "This package implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.") (license license:gpl3))) (define-public r-destiny (package (name "r-destiny") (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-ggplot-multistats" ,r-ggplot-multistats) ("r-ggplot2" ,r-ggplot2) ("r-ggthemes" ,r-ggthemes) ("r-irlba" ,r-irlba) ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcpphnsw" ,r-rcpphnsw) ("r-rspectra" ,r-rspectra) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-vim" ,r-vim))) (native-inputs `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes (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 "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description "This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.") (license license:agpl3+))) (define-public r-chipexoqual (package (name "r-chipexoqual") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-biovizbase" ,r-biovizbase) ("r-broom" ,r-broom) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-hexbin" ,r-hexbin) ("r-iranges" ,r-iranges) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rmarkdown" ,r-rmarkdown) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description "This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.") (license license:gpl2+))) (define-public r-copynumber (package (name "r-copynumber") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) (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 "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) (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 . "HTSCluster"))) (build-system r-build-system) (propagated-inputs `(("r-capushe" ,r-capushe) ("r-edger" ,r-edger) ("r-plotrix" ,r-plotrix))) (home-page "https://cran.r-project.org/web/packages/HTSCluster") (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") (description "This package provides a Poisson mixture model is implemented to cluster genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).") (license license:gpl3+))) (define-public r-deds (package (name "r-deds") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEDS" version)) (sha256 (base32 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) (properties `((upstream-name . "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. (define-public r-nbpseq (package (name "r-nbpseq") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "NBPSeq" version)) (sha256 (base32 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs `(("r-qvalue" ,r-qvalue))) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description "This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.") (license license:gpl2))) (define-public r-ebseq (package (name "r-ebseq") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs `(("r-blockmodeling" ,r-blockmodeling) ("r-gplots" ,r-gplots) ("r-testthat" ,r-testthat))) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description "This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data") (license license:artistic2.0))) (define-public r-karyoploter (package (name "r-karyoploter") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-bamsignals" ,r-bamsignals) ("r-bezier" ,r-bezier) ("r-biovizbase" ,r-biovizbase) ("r-digest" ,r-digest) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-memoise" ,r-memoise) ("r-regioner" ,r-regioner) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimics many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates.") (license license:artistic2.0))) (define-public r-lpsymphony (package (name "r-lpsymphony") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description "This package was derived from Rsymphony. 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 "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-fdrtool" ,r-fdrtool) ("r-lpsymphony" ,r-lpsymphony) ("r-slam" ,r-slam))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.") (license license:artistic2.0))) (define-public r-icobra (package (name "r-icobra") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-ggplot2" ,r-ggplot2) ("r-limma" ,r-limma) ("r-reshape2" ,r-reshape2) ("r-rocr" ,r-rocr) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinybs" ,r-shinybs) ("r-shinydashboard" ,r-shinydashboard) ("r-upsetr" ,r-upsetr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description "This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.") (license license:gpl2+))) (define-public r-mast (package (name "r-mast") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description "This package provides methods and models for handling zero-inflated single cell assay data.") (license license:gpl2+))) (define-public r-monocle (package (name "r-monocle") (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocviews" ,r-biocviews) ("r-cluster" ,r-cluster) ("r-combinat" ,r-combinat) ("r-ddrtree" ,r-ddrtree) ("r-densityclust" ,r-densityclust) ("r-dplyr" ,r-dplyr) ("r-fastica" ,r-fastica) ("r-ggplot2" ,r-ggplot2) ("r-hsmmsinglecell" ,r-hsmmsinglecell) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-limma" ,r-limma) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-pheatmap" ,r-pheatmap) ("r-plyr" ,r-plyr) ("r-proxy" ,r-proxy) ("r-qlcmatrix" ,r-qlcmatrix) ("r-rann" ,r-rann) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) ("r-rtsne" ,r-rtsne) ("r-slam" ,r-slam) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-vgam" ,r-vgam) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description "Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) (define-public r-monocle3 (package (name "r-monocle3") (version "0.1.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/monocle3") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-grr" ,r-grr) ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-limma" ,r-limma) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-matrix-utils" ,r-matrix-utils) ("r-pbapply" ,r-pbapply) ("r-pbmcapply" ,r-pbmcapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) ("r-pryr" ,r-pryr) ("r-proxy" ,r-proxy) ("r-pscl" ,r-pscl) ("r-purrr" ,r-purrr) ("r-rann" ,r-rann) ("r-rcpp" ,r-rcpp) ("r-rcppparallel" ,r-rcppparallel) ("r-reshape2" ,r-reshape2) ("r-reticulate" ,r-reticulate) ("r-rhpcblasctl" ,r-rhpcblasctl) ("r-rtsne" ,r-rtsne) ("r-shiny" ,r-shiny) ("r-slam" ,r-slam) ("r-spdep" ,r-spdep) ("r-speedglm" ,r-speedglm) ("r-stringr" ,r-stringr) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-uwot" ,r-uwot) ("r-viridis" ,r-viridis))) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") (license license:expat))) (define-public r-noiseq (package (name "r-noiseq") (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description "This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. It also supports the analysis of differential expression between two experimental conditions with no parametric assumptions.") (license license:artistic2.0))) (define-public r-scdd (package (name "r-scdd") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs `(("r-arm" ,r-arm) ("r-biocparallel" ,r-biocparallel) ("r-ebseq" ,r-ebseq) ("r-fields" ,r-fields) ("r-ggplot2" ,r-ggplot2) ("r-mclust" ,r-mclust) ("r-outliers" ,r-outliers) ("r-s4vectors" ,r-s4vectors) ("r-scran" ,r-scran) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description "This package implements a method to analyze single-cell RNA-seq data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.") (license license:gpl2))) (define-public r-scone (package (name "r-scone") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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.") (license license:artistic2.0))) (define-public r-geoquery (package (name "r-geoquery") (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-readr" ,r-readr) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.") (license license:gpl2))) (define-public r-illuminaio (package (name "r-illuminaio") (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) (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.") (license license:gpl2))) (define-public r-siggenes (package (name "r-siggenes") (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-multtest" ,r-multtest) ("r-scrime" ,r-scrime))) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") (description "This package provides tools for the identification of differentially expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) (define-public r-bumphunter (package (name "r-bumphunter") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) (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 "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) (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 "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap) ("r-apcluster" ,r-apcluster) ("r-ellipse" ,r-ellipse) ("r-fastcluster" ,r-fastcluster) ("r-fpc" ,r-fpc) ("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-gmodels" ,r-gmodels) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) ("r-mass" ,r-mass) ("r-mclust" ,r-mclust) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rtsne" ,r-rtsne) ("r-statmod" ,r-statmod) ("r-vegan" ,r-vegan) ("r-zoo" ,r-zoo))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. 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 "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bit64" ,r-bit64) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-rhdf5" ,r-rhdf5) ("r-shortread" ,r-shortread) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xvector" ,r-xvector))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description "IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) ;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-gkmsvm (package (name "r-gkmsvm") (version "0.81.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab) ("r-rcpp" ,r-rcpp) ("r-rocr" ,r-rocr) ("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+))) ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package (name "r-mutoss") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs `(("r-multcomp" ,r-multcomp) ("r-multtest" ,r-multtest) ("r-mvtnorm" ,r-mvtnorm) ("r-plotrix" ,r-plotrix))) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description "This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) ;; This is a CRAN package, but it depends on mutoss, which depends on multtest ;; from Bioconductor, so we put it here. (define-public r-metap (package (name "r-metap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mutoss" ,r-mutoss) ("r-rdpack" ,r-rdpack) ("r-tfisher" ,r-tfisher))) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description "The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) (define-public r-triform (package (name "r-triform") (version "1.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (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 "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description "Explore, diagnose, and compare variant calls using filters. The VariantTools package supports a workflow for loading data, calling single sample variants and tumor-specific somatic mutations or other sample-specific variant types (e.g., RNA editing). Most of the functions operate on alignments (BAM files) or datasets of called variants. The user is expected to have already aligned the reads with a separate tool, e.g., GSNAP via gmapR.") (license license:artistic2.0))) (define-public r-heatplus (package (name "r-heatplus") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description "This package provides tools to display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.") (license license:gpl2+))) (define-public r-gosemsim (package (name "r-gosemsim") (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-go-db" ,r-go-db) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.") (license license:artistic2.0))) (define-public r-anota (package (name "r-anota") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) ("r-qvalue" ,r-qvalue))) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description "Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) (define-public r-sigpathway (package (name "r-sigpathway") (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") (synopsis "Pathway analysis") (description "This package is used to conduct pathway analysis by calculating the NT_k and NE_k statistics in a statistical framework for determining whether a specified group of genes for a pathway has a coordinated association with a phenotype of interest.") (license license:gpl2))) (define-public r-fgsea (package (name "r-fgsea") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biocparallel" ,r-biocparallel) ("r-data-table" ,r-data-table) ("r-fastmatch" ,r-fastmatch) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.") (license license:expat))) (define-public r-dose (package (name "r-dose") (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocparallel" ,r-biocparallel) ("r-do-db" ,r-do-db) ("r-fgsea" ,r-fgsea) ("r-ggplot2" ,r-ggplot2) ("r-gosemsim" ,r-gosemsim) ("r-qvalue" ,r-qvalue) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description "This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang, respectively, for measuring semantic similarities among @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.") (license license:artistic2.0))) (define-public r-enrichplot (package (name "r-enrichplot") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dose" ,r-dose) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) ("r-gosemsim" ,r-gosemsim) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scatterpie" ,r-scatterpie) ("r-shadowtext" ,r-shadowtext))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description "The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics.") (license license:artistic2.0))) (define-public r-clusterprofiler (package (name "r-clusterprofiler") (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dose" ,r-dose) ("r-downloader" ,r-downloader) ("r-dplyr" ,r-dplyr) ("r-enrichplot" ,r-enrichplot) ("r-go-db" ,r-go-db) ("r-gosemsim" ,r-gosemsim) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-qvalue" ,r-qvalue) ("r-rlang" ,r-rlang) ("r-rvcheck" ,r-rvcheck) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description "This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.") (license license:artistic2.0))) (define-public r-mlinterfaces (package (name "r-mlinterfaces") (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cluster" ,r-cluster) ("r-fpc" ,r-fpc) ("r-gbm" ,r-gbm) ("r-gdata" ,r-gdata) ("r-genefilter" ,r-genefilter) ("r-ggvis" ,r-ggvis) ("r-hwriter" ,r-hwriter) ("r-mass" ,r-mass) ("r-mlbench" ,r-mlbench) ("r-pls" ,r-pls) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rpart" ,r-rpart) ("r-sfsmisc" ,r-sfsmisc) ("r-shiny" ,r-shiny) ("r-threejs" ,r-threejs))) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description "This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.") ;; Any version of the LGPL. (license license:lgpl2.1+))) (define-public r-annaffy (package (name "r-annaffy") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'remove-reference-to-non-free-data (lambda _ (substitute* "DESCRIPTION" ((", KEGG.db") "")) #t))))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-dbi" ,r-dbi) ("r-go-db" ,r-go-db))) (home-page "https://bioconductor.org/packages/annaffy/") (synopsis "Annotation tools for Affymetrix biological metadata") (description "This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.") ;; Any version of the LGPL according to the DESCRIPTION file. A copy of ;; the LGPL 2.1 is included. (license license:lgpl2.1+))) (define-public r-a4core (package (name "r-a4core") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-glmnet" ,r-glmnet))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description "This is the core package for the automated analysis of Affymetrix arrays.") (license license:gpl3))) (define-public r-a4classif (package (name "r-a4classif") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs `(("r-a4core" ,r-a4core) ("r-a4preproc" ,r-a4preproc) ("r-biobase" ,r-biobase) ("r-glmnet" ,r-glmnet) ("r-pamr" ,r-pamr) ("r-rocr" ,r-rocr) ("r-varselrf" ,r-varselrf))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description "This is the classification package for the automated analysis of Affymetrix arrays.") (license license:gpl3))) (define-public r-a4preproc (package (name "r-a4preproc") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description "This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.") (license license:gpl3))) (define-public r-a4reporting (package (name "r-a4reporting") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs `(("r-xtable" ,r-xtable))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description "This is a package for the automated analysis of Affymetrix arrays. It provides reporting features.") (license license:gpl3))) (define-public r-a4base (package (name "r-a4base") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs `(("r-a4core" ,r-a4core) ("r-a4preproc" ,r-a4preproc) ("r-annaffy" ,r-annaffy) ("r-biobase" ,r-biobase) ("r-genefilter" ,r-genefilter) ("r-glmnet" ,r-glmnet) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-mpm" ,r-mpm) ("r-multtest" ,r-multtest))) (home-page "https://bioconductor.org/packages/a4Base/") (synopsis "Automated Affymetrix array analysis base package") (description "This package provides basic features for the automated analysis of Affymetrix arrays.") (license license:gpl3))) (define-public r-a4 (package (name "r-a4") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) ("r-a4classif" ,r-a4classif) ("r-a4core" ,r-a4core) ("r-a4preproc" ,r-a4preproc) ("r-a4reporting" ,r-a4reporting))) (home-page "https://bioconductor.org/packages/a4/") (synopsis "Automated Affymetrix array analysis umbrella package") (description "This package provides a software suite for the automated analysis of Affymetrix arrays.") (license license:gpl3))) (define-public r-abseqr (package (name "r-abseqr") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc))) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-biocstyle" ,r-biocstyle) ("r-circlize" ,r-circlize) ("r-flexdashboard" ,r-flexdashboard) ("r-ggcorrplot" ,r-ggcorrplot) ("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-knitr" ,r-knitr) ("r-plotly" ,r-plotly) ("r-plyr" ,r-plyr) ("r-png" ,r-png) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-rmarkdown" ,r-rmarkdown) ("r-stringr" ,r-stringr) ("r-vegan" ,r-vegan) ("r-venndiagram" ,r-venndiagram))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description "AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. AbseqR empowers the users of abseqPy with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.") (license license:gpl3))) (define-public r-bacon (package (name "r-bacon") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-ellipse" ,r-ellipse) ("r-ggplot2" ,r-ggplot2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description "Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.") (license license:gpl2+))) (define-public r-rgadem (package (name "r-rgadem") (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-seqlogo" ,r-seqlogo))) (home-page "https://bioconductor.org/packages/rGADEM/") (synopsis "De novo sequence motif discovery") (description "rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.") (license license:artistic2.0))) (define-public r-motiv (package (name "r-motiv") (version "1.43.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-rgadem" ,r-rgadem) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/MotIV/") (synopsis "Motif identification and validation") (description "This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.") (license license:gpl2))) (define-public r-motifdb (package (name "r-motifdb") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-splitstackshape" ,r-splitstackshape))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.") (license license:artistic2.0))) (define-public r-motifbreakr (package (name "r-motifbreakr") (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-grimport" ,r-grimport) ("r-gviz" ,r-gviz) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-motifdb" ,r-motifdb) ("r-motifstack" ,r-motifstack) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tfmpvalue" ,r-tfmpvalue) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. This package gives a choice of algorithms for interrogation of genomes with motifs from public sources: @enumerate @item a weighted-sum probability matrix; @item log-probabilities; @item weighted by relative entropy. @end enumerate This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.") (license license:gpl2+))) (define-public r-motifstack (package (name "r-motifstack") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-biostrings" ,r-biostrings) ("r-ggplot2" ,r-ggplot2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description "The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.") (license license:gpl2+))) (define-public r-genomicscores (package (name "r-genomicscores") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs `(("r-annotationhub" ,r-annotationhub) ("r-biobase" ,r-biobase) ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) ("r-rhdf5" ,r-rhdf5) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description "This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.") (license license:artistic2.0))) (define-public r-atacseqqc (package (name "r-atacseqqc") (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-chippeakanno" ,r-chippeakanno) ("r-edger" ,r-edger) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-genomicscores" ,r-genomicscores) ("r-iranges" ,r-iranges) ("r-kernsmooth" ,r-kernsmooth) ("r-limma" ,r-limma) ("r-motifstack" ,r-motifstack) ("r-preseqr" ,r-preseqr) ("r-randomforest" ,r-randomforest) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description "ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. The ATACseqQC package was developed to help users to quickly assess whether their ATAC-seq experiment is successful. It includes diagnostic plots of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.") (license license:gpl2+))) (define-public r-gofuncr (package (name "r-gofuncr") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-genomicranges" ,r-genomicranges) ("r-gtools" ,r-gtools) ("r-iranges" ,r-iranges) ("r-mapplots" ,r-mapplots) ("r-rcpp" ,r-rcpp) ("r-vioplot" ,r-vioplot))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description "GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is included in the package and updated regularly. 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 "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) (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 "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) (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 "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description "AUCell identifies 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 "4.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) (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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 acquired 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 "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description "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 "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-corrplot" ,r-corrplot) ("r-dendextend" ,r-dendextend) ("r-doparallel" ,r-doparallel) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) ("r-limsolve" ,r-limsolve) ("r-magrittr" ,r-magrittr) ("r-pmcmr" ,r-pmcmr) ("r-pracma" ,r-pracma) ("r-reshape2" ,r-reshape2) ("r-somaticsignatures" ,r-somaticsignatures) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description "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 "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) (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 binding is expected.") ;; Any version of the LGPL (license license:lgpl2.1+))) (define-public r-simpleaffy (package (name "r-simpleaffy") (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (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 "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) (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 "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) (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 "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-mscoreutils" ,r-mscoreutils) ("r-msnbase" ,r-msnbase) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-robustbase" ,r-robustbase) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description "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 "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description "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 "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) (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 package 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 "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description "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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description "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 "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) (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))) (define-public r-biocfilecache (package (name "r-biocfilecache") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-dbi" ,r-dbi) ("r-dbplyr" ,r-dbplyr) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs) ("r-rsqlite" ,r-rsqlite))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description "This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.") (license license:artistic2.0))) (define-public r-iclusterplus (package (name "r-iclusterplus") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description "iClusterPlus is developed for integrative clustering analysis of multi-type genomic data and is an enhanced version of iCluster proposed and developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise from the experiments where biological samples (e.g. tumor samples) are analyzed by multiple techniques, for instance, @dfn{array comparative genomic hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so on. In the iClusterPlus model, binary observations such as somatic mutation are modeled as Binomial processes; categorical observations such as copy number states are realizations of Multinomial random variables; counts are modeled as Poisson random processes; and continuous measures are modeled by Gaussian distributions.") (license license:gpl2+))) (define-public r-rbowtie (package (name "r-rbowtie") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description "This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool.") (license license:artistic2.0))) (define-public r-sgseq (package (name "r-sgseq") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-igraph" ,r-igraph) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description "SGSeq is a package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.") (license license:artistic2.0))) (define-public r-rhisat2 (package (name "r-rhisat2") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ (substitute* "src/Makefile" (("`hostname`") "guix") (("`date`") "0") ;; Avoid shelling out to "which". (("^CC =.*") (which "gcc")) (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-sgseq" ,r-sgseq))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description "This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.") (license license:gpl3))) (define-public r-quasr (package (name "r-quasr") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rbowtie" ,r-rbowtie) ("r-rhisat2" ,r-rhisat2) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description "This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.") (license license:gpl2))) (define-public r-rqc (package (name "r-rqc") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biocstyle" ,r-biocstyle) ("r-biostrings" ,r-biostrings) ("r-biovizbase" ,r-biovizbase) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfiles" ,r-genomicfiles) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-knitr" ,r-knitr) ("r-markdown" ,r-markdown) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-shortread" ,r-shortread))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description "Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) (define-public r-birewire (package (name "r-birewire") (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-slam" ,r-slam) ("r-tsne" ,r-tsne))) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.") (license license:gpl3))) (define-public r-birta (package (name "r-birta") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limma" ,r-limma) ("r-mass" ,r-mass))) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description "Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-qqman" ,r-qqman) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description "This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.") (license license:expat))) (define-public r-ropls (package (name "r-ropls") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. This package provides imlementations of PCA, PLS, and OPLS for multivariate analysis and feature selection of omics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients).") (license license:cecill))) (define-public r-biosigner (package (name "r-biosigner") (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description "Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationhub" ,r-annotationhub) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-readr" ,r-readr) ("r-regioner" ,r-regioner) ("r-reshape2" ,r-reshape2) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.") (license license:gpl3))) (define-public r-rsubread (package (name "r-rsubread") (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description "This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) (define-public r-flowutils (package (name "r-flowutils") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-flowcore" ,r-flowcore) ("r-graph" ,r-graph) ("r-runit" ,r-runit) ("r-xml" ,r-xml))) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description "This package provides utilities for flow cytometry data.") (license license:artistic2.0))) (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs `(("r-all" ,r-all) ("r-biobase" ,r-biobase) ("r-cluster" ,r-cluster))) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description "This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) (define-public r-cytolib (package (name "r-cytolib") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars.in" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (native-inputs `(("r-knitr" ,r-knitr) ("pkg-config" ,pkg-config))) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib))) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description "This package provides the core data structure and API to represent and interact with gated cytometry data.") (license license:artistic2.0))) (define-public r-flowcore (package (name "r-flowcore") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rprotobuflib" ,r-rprotobuflib) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description "This package provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) (define-public r-flowmeans (package (name "r-flowmeans") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-feature" ,r-feature) ("r-flowcore" ,r-flowcore) ("r-rrcov" ,r-rrcov))) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description "This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) (define-public r-ncdfflow (package (name "r-ncdfflow") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-flowcore" ,r-flowcore) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) (define-public r-ggcyto (package (name "r-ggcyto") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-hexbin" ,r-hexbin) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description "With the dedicated fortify method implemented for @code{flowSet}, @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper and some custom layers also make it easy to add gates and population statistics to the plot.") (license license:artistic2.0))) (define-public r-flowviz (package (name "r-flowviz") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-flowcore" ,r-flowcore) ("r-hexbin" ,r-hexbin) ("r-idpmisc" ,r-idpmisc) ("r-kernsmooth" ,r-kernsmooth) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) (define-public r-flowclust (package (name "r-flowclust") (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-corpcor" ,r-corpcor) ("r-ellipse" ,r-ellipse) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) (inputs `(("gsl" ,gsl))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description "This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.") (license license:artistic2.0))) ;; TODO: this package bundles an old version of protobuf. It's not easy to ;; make it use our protobuf package instead. (define-public r-rprotobuflib (package (name "r-rprotobuflib") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) #t))))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description "This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.") (license license:bsd-3))) (define-public r-flowworkspace (package (name "r-flowworkspace") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-matrixstats" ,r-matrixstats) ("r-ncdfflow" ,r-ncdfflow) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description "This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.") (license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cluster" ,r-cluster) ("r-fda" ,r-fda) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-kernsmooth" ,r-kernsmooth) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rrcov" ,r-rrcov))) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description "This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the @code{flowCore} package.") (license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-data-table" ,r-data-table) ("r-flowclust" ,r-flowclust) ("r-flowcore" ,r-flowcore) ("r-flowstats" ,r-flowstats) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-graph" ,r-graph) ("r-gtools" ,r-gtools) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-r-utils" ,r-r-utils) ("r-rbgl" ,r-rbgl) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rrcov" ,r-rrcov))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars.in" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (inputs `(("libxml2" ,libxml2))) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggcyto" ,r-ggcyto) ("r-graph" ,r-graph) ("r-jsonlite" ,r-jsonlite) ("r-lattice" ,r-lattice) ("r-opencyto" ,r-opencyto) ("r-plyr" ,r-plyr) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-runit" ,r-runit) ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) ("r-xml2" ,r-xml2) ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description "This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.") (license license:artistic2.0))) (define-public r-flowsom (package (name "r-flowsom") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description "FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.") (license license:gpl2+))) (define-public r-mixomics (package (name "r-mixomics") (version "6.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) ("r-ggrepel" ,r-ggrepel) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description "mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gmodels" ,r-gmodels) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-mixomics" ,r-mixomics) ("r-moments" ,r-moments) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description "The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs `(("r-aucell" ,r-aucell) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-feather" ,r-feather) ("r-gseabase" ,r-gseabase) ("r-r-utils" ,r-r-utils) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the @dfn{transcription start site} (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-cicero (package (name "r-cicero") (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-glasso" ,r-glasso) ("r-gviz" ,r-gviz) ("r-igraph" ,r-igraph) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-monocle" ,r-monocle) ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vgam" ,r-vgam))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description "Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs `(("r-monocle3" ,r-monocle3) ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) (define-public r-cistopic (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") (revision "0")) (package (name "r-cistopic") (version (git-version "0.2.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) (build-system r-build-system) (propagated-inputs `(("r-aucell" ,r-aucell) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-dosnow" ,r-dosnow) ("r-dt" ,r-dt) ("r-feather" ,r-feather) ("r-fitdistrplus" ,r-fitdistrplus) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-lda" ,r-lda) ("r-matrix" ,r-matrix) ("r-plyr" ,r-plyr) ("r-rcistarget" ,r-rcistarget) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description "The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as @dfn{Latent Dirichlet Allocation} (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.") (license license:gpl3)))) (define-public r-genie3 (package (name "r-genie3") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description "This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.") (license license:gpl2+))) (define-public r-roc (package (name "r-roc") (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description "This package provides utilities for @dfn{Receiver Operating Characteristic} (ROC) curves, with a focus on micro arrays.") (license license:artistic2.0))) (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 (package (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") (version "0.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IlluminaHumanMethylation450kanno.ilmn12.hg19" version 'annotation)) (sha256 (base32 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) (properties `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) (build-system r-build-system) (propagated-inputs `(("r-minfi" ,r-minfi))) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") (synopsis "Annotation for Illumina's 450k methylation arrays") (description "This package provides manifests and annotation for Illumina's 450k array data.") (license license:artistic2.0))) (define-public r-watermelon (package (name "r-watermelon") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-illuminahumanmethylation450kanno-ilmn12-hg19" ,r-illuminahumanmethylation450kanno-ilmn12-hg19) ("r-illuminaio" ,r-illuminaio) ("r-limma" ,r-limma) ("r-lumi" ,r-lumi) ("r-matrixstats" ,r-matrixstats) ("r-methylumi" ,r-methylumi) ("r-roc" ,r-roc))) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description "The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the @code{methylumi} and @code{minfi} packages.") (license license:gpl3))) (define-public r-gdsfmt (package (name "r-gdsfmt") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. (snippet '(begin (for-each delete-file-recursively '("src/LZ4" "src/XZ" "src/ZLIB")) (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") (("(ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") "CoreArray/dVLIntGDS.o") (("PKG_LIBS = ./liblzma.a") "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) (string-append "include <" header ">"))) #t)))) (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs `(("lz4" ,lz4) ("xz" ,xz) ("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") (description "This package provides a high-level R interface to CoreArray @dfn{Genomic Data Structure} (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The @code{gdsfmt} package offers efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package @code{parallel}.") (license license:lgpl3))) (define-public r-bigmelon (package (name "r-bigmelon") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-gdsfmt" ,r-gdsfmt) ("r-geoquery" ,r-geoquery) ("r-methylumi" ,r-methylumi) ("r-minfi" ,r-minfi) ("r-watermelon" ,r-watermelon))) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) (define-public r-seqbias (package (name "r-seqbias") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-rhtslib" ,r-rhtslib))) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") (version "0.99.20") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" version 'annotation)) (sha256 (base32 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) (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-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-bsgenome" ,r-bsgenome) ("r-biostrings" ,r-biostrings))) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") (description "This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).") (license license:artistic2.0))) (define-public r-reqon (package (name "r-reqon") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs `(("r-rjava" ,r-rjava) ("r-rsamtools" ,r-rsamtools) ("r-seqbias" ,r-seqbias))) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description "This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.") (license license:gpl2))) (define-public r-wavcluster (package (name "r-wavcluster") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-foreach" ,r-foreach) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-hmisc" ,r-hmisc) ("r-iranges" ,r-iranges) ("r-mclust" ,r-mclust) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-stringr" ,r-stringr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description "This package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package integrates RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs `(("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) ("r-ggplot2" ,r-ggplot2) ("r-hmisc" ,r-hmisc) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-proxy" ,r-proxy) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vegan" ,r-vegan) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description "This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.") (license license:lgpl3+))) (define-public r-variantfiltering (package (name "r-variantfiltering") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-dt" ,r-dt) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-genomicscores" ,r-genomicscores) ("r-graph" ,r-graph) ("r-gviz" ,r-gviz) ("r-iranges" ,r-iranges) ("r-rbgl" ,r-rbgl) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs) ("r-shinythemes" ,r-shinythemes) ("r-shinytree" ,r-shinytree) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation) ("r-xvector" ,r-xvector))) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description "Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.") (license license:artistic2.0))) (define-public r-genomegraphs (package (name "r-genomegraphs") (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeGraphs" version)) (sha256 (base32 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs `(("r-biomart" ,r-biomart))) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl 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. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.") (license license:artistic2.0))) (define-public r-wavetiling (package (name "r-wavetiling") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-genomegraphs" ,r-genomegraphs) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-oligo" ,r-oligo) ("r-oligoclasses" ,r-oligoclasses) ("r-preprocesscore" ,r-preprocesscore) ("r-waveslim" ,r-waveslim))) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description "This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.") (license license:gpl2+))) (define-public r-variancepartition (package (name "r-variancepartition") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocparallel" ,r-biocparallel) ("r-colorramps" ,r-colorramps) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gplots" ,r-gplots) ("r-iterators" ,r-iterators) ("r-limma" ,r-limma) ("r-lme4" ,r-lme4) ("r-lmertest" ,r-lmertest) ("r-mass" ,r-mass) ("r-pbkrtest" ,r-pbkrtest) ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description "This is a package providing tools to quantify and interpret multiple sources of biological and technical variation in gene expression experiments. It uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The package includes dream differential expression analysis for repeated measures.") (license license:gpl2+))) (define-public r-htqpcr (package (name "r-htqpcr") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).") (license license:artistic2.0))) (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-htqpcr" ,r-htqpcr))) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs (package (name "r-activedriverwgs") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) (properties `((upstream-name . "ActiveDriverWGS"))) (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-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description "This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.") (license license:gpl3))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activepathways (package (name "r-activepathways") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-ggplot2" ,r-ggplot2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description "This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.") (license license:gpl3))) (define-public r-bgmix (package (name "r-bgmix") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth))) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description "This package provides fully Bayesian mixture models for differential gene expression.") (license license:gpl2))) (define-public r-bgx (package (name "r-bgx") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-gcrma" ,r-gcrma) ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description "This package provides tools for Bayesian integrated analysis of Affymetrix GeneChips.") (license license:gpl2))) (define-public r-bhc (package (name "r-bhc") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") (synopsis "Bayesian hierarchical clustering") (description "The method implemented in this package performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.") (license license:gpl3))) (define-public r-bicare (package (name "r-bicare") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-gseabase" ,r-gseabase) ("r-multtest" ,r-multtest))) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description "This is a package for biclustering analysis and exploration of results.") (license license:gpl2))) (define-public r-bifet (package (name "r-bifet") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-poibin" ,r-poibin))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias.") (license license:gpl3))) (define-public r-rsbml (package (name "r-rsbml") (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs `(("libsbml" ,libsbml) ("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description "This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (license license:artistic2.0))) (define-public r-hypergraph (package (name "r-hypergraph") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description "This package implements some simple capabilities for representing and manipulating hypergraphs.") (license license:artistic2.0))) (define-public r-hyperdraw (package (name "r-hyperdraw") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) (propagated-inputs `(("r-graph" ,r-graph) ("r-hypergraph" ,r-hypergraph) ("r-rgraphviz" ,r-rgraphviz))) (home-page "https://bioconductor.org/packages/hyperdraw") (synopsis "Visualizing hypergraphs") (description "This package provides functions for visualizing hypergraphs.") (license license:gpl2+))) (define-public r-biggr (package (name "r-biggr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs `(("r-hyperdraw" ,r-hyperdraw) ("r-hypergraph" ,r-hypergraph) ("r-lim" ,r-lim) ("r-limsolve" ,r-limsolve) ("r-rsbml" ,r-rsbml) ("r-stringr" ,r-stringr))) (home-page "https://bioconductor.org/packages/BiGGR/") (synopsis "Constraint based modeling using metabolic reconstruction databases") (description "This package provides an interface to simulate metabolic reconstruction from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic reconstruction databases. The package facilitates @dfn{flux balance analysis} (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.") (license license:gpl3+))) (define-public r-bigmemoryextras (package (name "r-bigmemoryextras") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmemoryExtras" version)) (sha256 (base32 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj")))) (properties `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs `(("r-bigmemory" ,r-bigmemory))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds safety and convenience features to the @code{filebacked.big.matrix} class from the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a file-system-based permissions system. Utilities are provided for using @code{BigMatrix}-derived classes as @code{assayData} matrices within the @code{Biobase} package's @code{eSet} family of classes. @code{BigMatrix} provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, a file-backed matrix with factor properties.") (license license:artistic2.0))) (define-public r-bigpint (package (name "r-bigpint") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs `(("r-delayedarray" ,r-delayedarray) ("r-dplyr" ,r-dplyr) ("r-ggally" ,r-ggally) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-hexbin" ,r-hexbin) ("r-hmisc" ,r-hmisc) ("r-htmlwidgets" ,r-htmlwidgets) ("r-plotly" ,r-plotly) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-shiny" ,r-shiny) ("r-shinycssloaders" ,r-shinycssloaders) ("r-shinydashboard" ,r-shinydashboard) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description "This package provides methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.") (license license:gpl3))) (define-public r-chemminer (package (name "r-chemminer") (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-digest" ,r-digest) ("r-dt" ,r-dt) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-png" ,r-png) ("r-rcpp" ,r-rcpp) ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) ("r-rsvg" ,r-rsvg))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description "ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.") (license license:artistic2.0))) (define-public r-bioassayr (package (name "r-bioassayr") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-chemminer" ,r-chemminer) ("r-dbi" ,r-dbi) ("r-matrix" ,r-matrix) ("r-rjson" ,r-rjson) ("r-rsqlite" ,r-rsqlite) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/TylerBackman/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description "bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of @dfn{high throughput screening fingerprints} (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.") (license license:artistic2.0))) (define-public r-biobroom (package (name "r-biobroom") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description "This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to @code{tidy} data. It thus serves as a complement to the @code{broom} package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-graphite (package (name "r-graphite") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-checkmate" ,r-checkmate) ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs))) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description "Graphite provides networks derived from eight public pathway databases, and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols).") (license license:agpl3+))) (define-public r-reactomepa (package (name "r-reactomepa") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dose" ,r-dose) ("r-enrichplot" ,r-enrichplot) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) ("r-graphite" ,r-graphite) ("r-igraph" ,r-igraph) ("r-reactome-db" ,r-reactome-db))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description "This package provides functions for pathway analysis based on the REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.") (license license:gpl2))) (define-public r-ebarrays (package (name "r-ebarrays") (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-cluster" ,r-cluster) ("r-lattice" ,r-lattice))) (home-page "https://bioconductor.org/packages/EBarrays/") (synopsis "Gene clustering and differential expression identification") (description "EBarrays provides tools for the analysis of replicated/unreplicated microarray data.") (license license:gpl2+))) (define-public r-bioccasestudies (package (name "r-bioccasestudies") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCaseStudies" version)) (sha256 (base32 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1")))) (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/BiocCaseStudies") (synopsis "Support for the case studies monograph") (description "This package provides software and data to support the case studies monograph.") (license license:artistic2.0))) (define-public r-biocgraph (package (name "r-biocgraph") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-geneplotter" ,r-geneplotter) ("r-graph" ,r-graph) ("r-rgraphviz" ,r-rgraphviz))) (home-page "https://bioconductor.org/packages/biocGraph/") (synopsis "Graph examples and use cases in Bioinformatics") (description "This package provides examples and code that make use of the different graph related packages produced by Bioconductor.") (license license:artistic2.0))) (define-public r-experimenthub (package (name "r-experimenthub") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs `(("r-annotationhub" ,r-annotationhub) ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-curl" ,r-curl) ("r-rappdirs" ,r-rappdirs) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description "This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description "MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from @code{SummarizedExperiment}, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.") (license license:artistic2.0))) (define-public r-bioconcotk (package (name "r-bioconcotk") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs `(("r-bigrquery" ,r-bigrquery) ("r-car" ,r-car) ("r-complexheatmap" ,r-complexheatmap) ("r-curatedtcgadata" ,r-curatedtcgadata) ("r-dbi" ,r-dbi) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-iranges" ,r-iranges) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-rgraphviz" ,r-rgraphviz) ("r-rjson" ,r-rjson) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description "The purpose of this package is to provide a central interface to various tools for genome-scale analysis of cancer studies.") (license license:artistic2.0))) (define-public r-biocor (package (name "r-biocor") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-gseabase" ,r-gseabase) ("r-matrix" ,r-matrix))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description "This package provides tools to calculate functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships, and so on.") (license license:expat))) (define-public r-biocpkgtools (package (name "r-biocpkgtools") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs `(("r-biocfilecache" ,r-biocfilecache) ("r-biocmanager" ,r-biocmanager) ("r-biocviews" ,r-biocviews) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-gh" ,r-gh) ("r-graph" ,r-graph) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-httr" ,r-httr) ("r-igraph" ,r-igraph) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-rappdirs" ,r-rappdirs) ("r-rbgl" ,r-rbgl) ("r-readr" ,r-readr) ("r-rex" ,r-rex) ("r-rlang" ,r-rlang) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description "Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.") (license license:expat))) (define-public r-biocset (package (name "r-biocset") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocio" ,r-biocio) ("r-dplyr" ,r-dplyr) ("r-keggrest" ,r-keggrest) ("r-ontologyindex" ,r-ontologyindex) ("r-plyr" ,r-plyr) ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis "Representing Different Biological Sets") (description "BiocSet displays different biological sets in a triple tibble format. These three tibbles are @code{element}, @code{set}, and @code{elementset}. The user has the ability to activate one of these three tibbles to perform common functions from the @code{dplyr} package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.") (license license:artistic2.0))) (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) (propagated-inputs `(("r-biocstyle" ,r-biocstyle) ("r-bookdown" ,r-bookdown) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-stringr" ,r-stringr) ("r-usethis" ,r-usethis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") (synopsis "Tools to aid the development of Bioconductor Workflow packages") (description "This package provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (license license:expat))) (define-public r-biodist (package (name "r-biodist") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-kernsmooth" ,r-kernsmooth))) (home-page "https://bioconductor.org/packages/bioDist/") (synopsis "Different distance measures") (description "This package provides a collection of software tools for calculating distance measures.") (license license:artistic2.0))) (define-public r-pcatools (package (name "r-pcatools") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-bh" ,r-bh) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) ("r-cowplot" ,r-cowplot) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-lattice" ,r-lattice) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description "@dfn{Principal Component Analysis} (PCA) extracts the fundamental structure of the data without the need to build any model to represent it. This \"summary\" of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via @code{BiocSingular}; users can also identify an optimal number of principal components via different metrics, such as the elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.") (license license:gpl3))) (define-public r-rgreat (package (name "r-rgreat") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description "This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.") (license license:expat))) (define-public r-m3c (package (name "r-m3c") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-corpcor" ,r-corpcor) ("r-doparallel" ,r-doparallel) ("r-dosnow" ,r-dosnow) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) ("r-matrixcalc" ,r-matrixcalc) ("r-rtsne" ,r-rtsne) ("r-umap" ,r-umap))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/M3C") (synopsis "Monte Carlo reference-based consensus clustering") (description "M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of @code{K} and can reject the null hypothesis @code{K=1}.") (license license:agpl3+))) (define-public r-icens (package (name "r-icens") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival))) (home-page "https://bioconductor.org/packages/Icens") (synopsis "NPMLE for censored and truncated data") (description "This package provides many functions for computing the @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and truncated data.") (license license:artistic2.0))) ;; This is a CRAN package but it depends on r-icens, which is published on ;; Bioconductor. (define-public r-interval (package (name "r-interval") (version "1.1-0.7") (source (origin (method url-fetch) (uri (cran-uri "interval" version)) (sha256 (base32 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs `(("r-icens" ,r-icens) ("r-mlecens" ,r-mlecens) ("r-perm" ,r-perm) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/interval/") (synopsis "Weighted Logrank tests and NPMLE for interval censored data") (description "This package provides functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on r-interval, which depends on a ;; Bioconductor package. (define-public r-fhtest (package (name "r-fhtest") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "FHtest" version)) (sha256 (base32 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs `(("r-interval" ,r-interval) ("r-kmsurv" ,r-kmsurv) ("r-mass" ,r-mass) ("r-perm" ,r-perm) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/FHtest/") (synopsis "Tests for survival data based on the Fleming-Harrington class") (description "This package provides functions to compare two or more survival curves with: @itemize @item The Fleming-Harrington test for right-censored data based on permutations and on counting processes. @item An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution. @end itemize ") (license license:gpl2+))) (define-public r-fourcseq (package (name "r-fourcseq") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FourCSeq" version)) (sha256 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb")))) (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-deseq2" ,r-deseq2) ("r-fda" ,r-fda) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggbio" ,r-ggbio) ("r-ggplot2" ,r-ggplot2) ("r-gtools" ,r-gtools) ("r-lsd" ,r-lsd) ("r-matrix" ,r-matrix) ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") (synopsis "Analysis of multiplexed 4C sequencing data") (description "This package is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a Python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.") (license license:gpl3+))) (define-public r-preprocesscore (package (name "r-preprocesscore") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) (home-page "https://github.com/bmbolstad/preprocessCore") (synopsis "Collection of pre-processing functions") (description "This package provides a library of core pre-processing and normalization routines.") (license license:lgpl2.0+))) ;; This is a CRAN package, but it depends on preprocessorcore, which is a ;; Bioconductor package. (define-public r-wgcna (package (name "r-wgcna") (version "1.69") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-doparallel" ,r-doparallel) ("r-dynamictreecut" ,r-dynamictreecut) ("r-fastcluster" ,r-fastcluster) ("r-foreach" ,r-foreach) ("r-go-db" ,r-go-db) ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) ("r-rcpp" ,r-rcpp) ("r-survival" ,r-survival) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore))) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") (description "This package provides functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. It includes functions for rudimentary data cleaning, construction and summarization of correlation networks, module identification and functions for relating both variables and modules to sample traits. It also includes a number of utility functions for data manipulation and visualization.") (license license:gpl2+))) (define-public r-rgraphviz (package (name "r-rgraphviz") (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ ;; The replacement value is taken from src/graphviz/builddate.h (substitute* "src/graphviz/configure" (("VERSION_DATE=.*") "VERSION_DATE=20200427.2341\n")) #t))))) ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-graph" ,r-graph))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description "This package interfaces R with the graphviz library for plotting R graph objects from the @code{graph} package.") (license license:epl1.0))) (define-public r-fithic (package (name "r-fithic") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-fdrtool" ,r-fdrtool) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description "Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.") (license license:gpl2+))) (define-public r-hitc (package (name "r-hitc") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) (properties `((upstream-name . "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-hdf5array (package (name "r-hdf5array") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5LIB_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.") (license license:artistic2.0))) (define-public r-rhdf5lib (package (name "r-rhdf5lib") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries (delete-file-recursively "src/wininclude/") (delete-file-recursively "src/winlib-4.9.3/") (delete-file-recursively "src/winlib-8.3.0/") (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'do-not-use-bundled-hdf5 (lambda* (#:key inputs #:allow-other-keys) (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" ((" \"%s/libsz.a\"") "")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) "hdf5") ;; Remove timestamp and host system information to make ;; the build reproducible. (substitute* "hdf5/src/libhdf5.settings.in" (("Configured on: @CONFIG_DATE@") "Configured on: Guix") (("Uname information:.*") "Uname information: Linux\n") ;; Remove unnecessary store reference. (("C Compiler:.*") "C Compiler: GCC\n")) (rename-file "hdf5/src/libhdf5.settings.in" "hdf5/src/libhdf5.settings") (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" (("@ZLIB_LIB@") "-lz") (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") (string-append "HDF5_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) (("HDF5_LIB=.*") (string-append "HDF5_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") (("HDF5_HL_LIB=.*") (string-append "HDF5_HL_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) (("HDF5_HL_CXX_LIB=.*") (string-append "HDF5_HL_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("hdf5" ,hdf5-1.10))) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R packages.") (license license:artistic2.0))) (define-public r-beachmat (package (name "r-beachmat") (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-matrix" ,r-matrix))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) (define-public r-scuttle (package (name "r-scuttle") (version "1.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-genomicranges" ,r-genomicranges) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description "This package provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. It also provides some helper functions to assist development of other packages.") (license license:gpl3))) (define-public r-scater (package (name "r-scater") (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-scuttle" ,r-scuttle) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.") (license license:gpl2+))) (define-public r-scran (package (name "r-scran") (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-bh" ,r-bh) ("r-biocgenerics" ,r-biocgenerics) ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) ("r-bluster" ,r-bluster) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-scuttle" ,r-scuttle) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-matrixgenerics" ,r-matrixgenerics) ("r-matrixstats" ,r-matrixstats) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description "This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.") (license license:expat))) (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-matrixgenerics" ,r-matrixgenerics) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors) ("r-sparsematrixstats" ,r-sparsematrixstats))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description "This package provides a port of the @code{matrixStats} API for use with @code{DelayedMatrix} objects from the @code{DelayedArray} package. It contains high-performing functions operating on rows and columns of @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) (define-public r-mscoreutils (package (name "r-mscoreutils") (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description "This package defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) (define-public r-biocio (package (name "r-biocio") (version "1.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-rcurl" ,r-rcurl) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description "This package implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.") (license license:artistic2.0))) (define-public r-msmseda (package (name "r-msmseda") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs `(("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-msnbase" ,r-msnbase) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page "https://bioconductor.org/packages/msmsEDA") (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") (description "Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.") (license license:gpl2))) (define-public r-msmstests (package (name "r-msmstests") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) ("r-msmseda" ,r-msmseda) ("r-msnbase" ,r-msnbase) ("r-qvalue" ,r-qvalue))) (home-page "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") (description "This packages provides statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.") (license license:gpl2))) (define-public r-catalyst (package (name "r-catalyst") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-consensusclusterplus" ,r-consensusclusterplus) ("r-cowplot" ,r-cowplot) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-drc" ,r-drc) ("r-flowcore" ,r-flowcore) ("r-flowsom" ,r-flowsom) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-ggridges" ,r-ggridges) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-nnls" ,r-nnls) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-rtsne" ,r-rtsne) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-scater" ,r-scater) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) (define-public r-kegggraph (package (name "r-kegggraph") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description "@code{r-kegggraph} is an interface between Kegg Pathway database and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated kgml (Kegg XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.") (license license:gpl2+))) (define-public r-pathview (package (name "r-pathview") (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-graph" ,r-graph) ("r-kegggraph" ,r-kegggraph) ("r-keggrest" ,r-keggrest) ("r-org-hs-eg-db" ,r-org-hs-eg-db) ("r-png" ,r-png) ("r-rgraphviz" ,r-rgraphviz) ("r-xml" ,r-xml))) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description "@code{r-pathview} is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. This package automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, @code{r-pathview} also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+)))