(define-public r-affycoretools
(package
(name "r-affycoretools")
- (version "1.58.2")
+ (version "1.58.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycoretools" version))
(sha256
(base32
- "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd"))))
+ "12r9ljkp3xix0xq8d1488c8wb3a4whb805v48ynmv985bs3phc71"))))
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.16.0")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9"))))
+ "03cf9c94ra4f847ndlf8sn2cq1kl1055514wjq0lqbvlbfdj1dq3"))))
(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-biocsingular
(package
(name "r-biocsingular")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "0qd7r2k56ym7ivjgapxbk7fyj2d7396f1ad1hkgnicgyw1an5q1r"))))
+ "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k"))))
(properties `((upstream-name . "BiocSingular")))
(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 "3.14.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk"))))
+ "1y1l3yf1r1ykl9ngipvyzl5hbxxsfz7z5q5rcywkyss2b2b6gsg8"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
(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/")
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 "1.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MultiAssayExperiment" version))
+ (sha256
+ (base32
+ "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc"))))
+ (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 "http://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 abilty 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