diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 573 |
1 files changed, 343 insertions, 230 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85ee56c539..33f66ce8be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -50,6 +50,33 @@ ;;; 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") @@ -72,35 +99,6 @@ database, assembled using data from REACTOME.") (license license:cc-by4.0))) -(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-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -571,30 +569,6 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") "This package exposes an annotation database generated from Ensembl.") (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-txdb-hsapiens-ucsc-hg19-knowngene (package (name "r-txdb-hsapiens-ucsc-hg19-knowngene") @@ -774,103 +748,6 @@ annotations.") "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") @@ -893,32 +770,6 @@ performing parallel computations on multicore machines.") 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") @@ -1027,6 +878,56 @@ All datasets are restricted to protein coding genes.") 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-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-hsmmsinglecell (package (name "r-hsmmsinglecell") @@ -1103,62 +1004,31 @@ examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) -(define-public r-coverageview +(define-public r-gagedata (package - (name "r-coverageview") - (version "1.28.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "CoverageView" version)) - (sha256 - (base32 - "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) + (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) - (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))) + (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 @@ -1236,6 +1106,189 @@ of 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-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-affycomp (package (name "r-affycomp") @@ -9187,3 +9240,63 @@ 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+))) |