;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
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")
`(("r-bsgenome" ,r-bsgenome)
("r-bsgenome-mmusculus-ucsc-mm9"
,r-bsgenome-mmusculus-ucsc-mm9)))
- (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
+ (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
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.7")
+ (version "3.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
version 'annotation))
(sha256
(base32
- "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
+ "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
+;; 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 "0.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NMF" version))
+ (sha256
+ (base32
+ "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
+ (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)))
+ (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")
(define-public r-affycoretools
(package
(name "r-affycoretools")
- (version "1.58.2")
+ (version "1.58.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycoretools" version))
(sha256
(base32
- "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd"))))
+ "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
("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)
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya"))))
+ "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-systempiper" ,r-systempiper)))
- (home-page "http://bioconductor.org/packages/DiffBind")
+ (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
("r-rsamtools" ,r-rsamtools)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)))
- (home-page "http://bioconductor.org/packages/RIPSeeker")
+ (home-page "https://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
(description
("r-biocgenerics" ,r-biocgenerics)
("r-biobase" ,r-biobase)
("r-mass" ,r-mass)))
- (home-page "http://bioconductor.org/packages/multtest")
+ (home-page "https://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
"This package can do non-parametric bootstrap and permutation
"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+)))
+
(define-public r-codedepends
(package
(name "r-codedepends")
`(("r-codetools" ,r-codetools)
("r-graph" ,r-graph)
("r-xml" ,r-xml)))
- (home-page "http://cran.r-project.org/web/packages/CodeDepends")
+ (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
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.20.0")
+ (version "3.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
+ "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
("r-seqinr" ,r-seqinr)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-venndiagram" ,r-venndiagram)))
- (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
+ (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,
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
- (home-page "http://bioconductor.org/packages/marray")
+ (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,
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-marray" ,r-marray)))
- (home-page "http://bioconductor.org/packages/CGHbase")
+ (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.")
("r-impute" ,r-impute)
("r-dnacopy" ,r-dnacopy)
("r-snowfall" ,r-snowfall)))
- (home-page "http://bioconductor.org/packages/CGHcall")
+ (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.")
("r-matrixstats" ,r-matrixstats)
("r-r-utils" ,r-r-utils)
("r-rsamtools" ,r-rsamtools)))
- (home-page "http://bioconductor.org/packages/QDNAseq")
+ (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
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
+ "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.16.0")
+ (version "1.16.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9"))))
+ "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
("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)
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf"))))
+ "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocsingular
(package
(name "r-biocsingular")
- (version "1.2.0")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "0qd7r2k56ym7ivjgapxbk7fyj2d7396f1ad1hkgnicgyw1an5q1r"))))
+ "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
(define-public r-destiny
(package
(name "r-destiny")
- (version "3.0.0")
+ (version "3.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
- "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
+ "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://r-forge.r-project.org/projects/rsymphony")
+ (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
(define-public r-gkmsvm
(package
(name "r-gkmsvm")
- (version "0.79.0")
+ (version "0.80.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gkmSVM" version))
(sha256
(base32
- "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
+ "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
(properties `((upstream-name . "gkmSVM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernlab" ,r-kernlab)
+ `(("r-kernlab" ,r-kernlab)
("r-rcpp" ,r-rcpp)
("r-rocr" ,r-rocr)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)))
(home-page "https://cran.r-project.org/web/packages/gkmSVM")
(synopsis "Gapped-kmer support vector machine")
(define-public r-metap
(package
(name "r-metap")
- (version "1.2")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "metap" version))
(sha256
(base32
- "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
+ "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
(define-public r-heatplus
(package
(name "r-heatplus")
- (version "2.32.0")
+ (version "2.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
- "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
+ "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "1jblx00b869xhx1c4n9m2g1hqr00rm9ywr1hrlx42bdd8k5ax1xh"))))
+ "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
- (version "3.14.0")
+ (version "3.14.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk"))))
+ "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.66.0")
+ (version "1.66.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8"))))
+ "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
("r-mlbench" ,r-mlbench)
("r-pls" ,r-pls)
("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rda" ,r-rda)
("r-rpart" ,r-rpart)
("r-sfsmisc" ,r-sfsmisc)
("r-shiny" ,r-shiny)
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.34.0")
+ (version "2.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "14ylbrzb9haqwfdd9g813mzhll6gwvqf2r7cmbaxz5lkl0j0nglx"))))
+ "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))
(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/")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.10.1")
+ (version "1.10.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
+ "18zf90iksglbs13cwr4jjwsv332a19lf4bpdmy69jz8bpwrklv22"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
("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
(define-public r-yamss
(package
(name "r-yamss")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yamss" version))
(sha256
(base32
- "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky"))))
+ "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.8.1")
+ (version "3.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb"))))
+ "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-ropls
(package
(name "r-ropls")
- (version "1.18.0")
+ (version "1.18.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ropls" version))
(sha256
(base32
- "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp"))))
+ "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.0.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
+ "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(define-public r-flowworkspace
(package
(name "r-flowworkspace")
- (version "3.34.0")
+ (version "3.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowWorkspace" version))
(sha256
(base32
- "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762"))))
+ "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
(propagated-inputs
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.10.6")
+ (version "6.10.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
+ "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
(define-public r-depecher
(package
(name "r-depecher")
- (version "1.2.0")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
+ "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
("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
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.4.0")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
+ "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
("r-vgam" ,r-vgam)))
(home-page "https://bioconductor.org/packages/cicero/")
(synopsis "Predict cis-co-accessibility from single-cell data")
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.16.0")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8"))))
+ "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
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 "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ReactomePA" version))
+ (sha256
+ (base32
+ "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
+ (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)))
+ (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 "2.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EBarrays" version))
+ (sha256
+ (base32
+ "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
+ (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 "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocCaseStudies" version))
+ (sha256
+ (base32
+ "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
+ (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 "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biocGraph" version))
+ (sha256
+ (base32
+ "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
+ (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 "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ExperimentHub" version))
+ (sha256
+ (base32
+ "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
+ (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)))
+ (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 "1.12.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MultiAssayExperiment" version))
+ (sha256
+ (base32
+ "01cnp00y5bk551c8gqgqp5468dvccg72i0rvh5cxgbx1c42zy6xn"))))
+ (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)))
+ (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 "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocOncoTK" version))
+ (sha256
+ (base32
+ "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
+ (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)))
+ (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 "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BioCor" version))
+ (sha256
+ (base32
+ "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
+ (properties `((upstream-name . "BioCor")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-gseabase" ,r-gseabase)
+ ("r-matrix" ,r-matrix)))
+ (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 "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocPkgTools" version))
+ (sha256
+ (base32
+ "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53"))))
+ (properties `((upstream-name . "BiocPkgTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("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-rbgl" ,r-rbgl)
+ ("r-readr" ,r-readr)
+ ("r-rex" ,r-rex)
+ ("r-rvest" ,r-rvest)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-xml2" ,r-xml2)))
+ (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 "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocSet" version))
+ (sha256
+ (base32
+ "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
+ (properties `((upstream-name . "BiocSet")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dplyr" ,r-dplyr)
+ ("r-keggrest" ,r-keggrest)
+ ("r-plyr" ,r-plyr)
+ ("r-rlang" ,r-rlang)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-tibble" ,r-tibble)))
+ (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 "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocWorkflowTools" version))
+ (sha256
+ (base32
+ "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad"))))
+ (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)))
+ (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 "1.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bioDist" version))
+ (sha256
+ (base32
+ "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
+ (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)))
HCoop / jackhill / guix / guix.git / blobdiff