#: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)
\f
;;; Annotations
+(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")
package @code{affy}.")
(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)))
+
\f
;;; Packages
(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-destiny
(package
(name "r-destiny")
- (version "2.14.0")
+ (version "3.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
- "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
+ "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
(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-igraph" ,r-igraph)
+ ("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)))
(home-page "https://bioconductor.org/packages/destiny/")
(synopsis "Create and plot diffusion maps")
(define-public r-siggenes
(package
(name "r-siggenes")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "siggenes" version))
(sha256
(base32
- "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
+ "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(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/")
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 "1.46.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BGmix" version))
+ (sha256
+ (base32
+ "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
+ (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 "1.52.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bgx" version))
+ (sha256
+ (base32
+ "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
+ (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 "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BHC" version))
+ (sha256
+ (base32
+ "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
+ (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 "1.44.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BicARE" version))
+ (sha256
+ (base32
+ "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
+ (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 "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiFET" version))
+ (sha256
+ (base32
+ "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
+ (properties `((upstream-name . "BiFET")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-poibin" ,r-poibin)))
+ (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 "2.44.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rsbml" version))
+ (sha256
+ (base32
+ "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
+ (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 "1.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "hypergraph" version))
+ (sha256
+ (base32
+ "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
+ (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 "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "hyperdraw" version))
+ (sha256
+ (base32
+ "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
+ (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 "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiGGR" version))
+ (sha256
+ (base32
+ "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
+ (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 "1.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bigmemoryExtras" version))
+ (sha256
+ (base32
+ "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
+ (properties
+ `((upstream-name . "bigmemoryExtras")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bigmemory" ,r-bigmemory)))
+ (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 filesystem-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 "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bigPint" version))
+ (sha256
+ (base32
+ "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk"))))
+ (properties `((upstream-name . "bigPint")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("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-tidyr" ,r-tidyr)))
+ (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 "3.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ChemmineR" version))
+ (sha256
+ (base32
+ "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
+ (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)))
+ (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 "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bioassayR" version))
+ (sha256
+ (base32
+ "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
+ (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)))
+ (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 "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biobroom" version))
+ (sha256
+ (base32
+ "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
+ (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)))
+ (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 "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "graphite" version))
+ (sha256
+ (base32
+ "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
+ (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 "1.30.0")
+ (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 "1.12.1")
+ (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