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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 428 |
1 files changed, 428 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33f66ce8be..f1af34844f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-homo-sapiens + (package + (name "r-homo-sapiens") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Homo.sapiens" version 'annotation)) + (sha256 + (base32 + "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) + (properties + `((upstream-name . "Homo.sapiens"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) + ("r-organismdbi" ,r-organismdbi) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/Homo.sapiens/") + (synopsis "Annotation package for the Homo.sapiens object") + (description + "This package contains the Homo.sapiens object to access data from +several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -9241,6 +9268,296 @@ 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-erma + (package + (name "r-erma") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "erma" version)) + (sha256 + (base32 + "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/erma") + (synopsis "Epigenomic road map adventures") + (description + "The epigenomics road map describes locations of epigenetic marks in DNA +from a variety of cell types. Of interest are locations of histone +modifications, sites of DNA methylation, and regions of accessible chromatin. +This package presents a selection of elements of the road map including +metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines +by Ernst and Kellis.") + (license license:artistic2.0))) + +(define-public r-ggbio + (package + (name "r-ggbio") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-organismdbi" ,r-organismdbi) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://www.tengfei.name/ggbio/") + (synopsis "Visualization tools for genomic data") + (description + "The ggbio package extends and specializes the grammar of graphics for +biological data. The graphics are designed to answer common scientific +questions, in particular those often asked of high throughput genomics data. +All core Bioconductor data structures are supported, where appropriate. The +package supports detailed views of particular genomic regions, as well as +genome-wide overviews. Supported overviews include ideograms and grand linear +views. High-level plots include sequence fragment length, edge-linked +interval to data view, mismatch pileup, and several splicing summaries.") + (license license:artistic2.0))) + +(define-public r-gqtlbase + (package + (name "r-gqtlbase") + (version "1.21.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLBase" version)) + (sha256 + (base32 + "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) + (properties `((upstream-name . "gQTLBase"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This is an upstream bug. + (add-after 'unpack 'fix-imports + (lambda _ + (substitute* "NAMESPACE" + ((".*maxffmode.*") "") + (("importFrom\\(ff,.*") "import(ff)\n")) + #t))))) + (propagated-inputs + `(("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-biocgenerics" ,r-biocgenerics) + ("r-bit" ,r-bit) + ("r-doparallel" ,r-doparallel) + ("r-ff" ,r-ff) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLBase") + (synopsis "Infrastructure for eQTL, mQTL and similar studies") + (description + "The purpose of this package is to simplify the storage and interrogation +of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, +and more.") + (license license:artistic2.0))) + +(define-public r-gqtlstats + (package + (name "r-gqtlstats") + (version "1.21.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLstats" version)) + (sha256 + (base32 + "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) + (properties `((upstream-name . "gQTLstats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-beeswarm" ,r-beeswarm) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-erma" ,r-erma) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-gqtlbase" ,r-gqtlbase) + ("r-hardyweinberg" ,r-hardyweinberg) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-mgcv" ,r-mgcv) + ("r-plotly" ,r-plotly) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-snpstats" ,r-snpstats) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLstats") + (synopsis "Computationally efficient analysis for eQTL and allied studies") + (description + "This package provides tools for the computationally efficient analysis +of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. +The software in this package aims to support refinements and functional +interpretation of members of a collection of association statistics on a +family of feature/genome hypotheses.") + (license license:artistic2.0))) + +(define-public r-gviz + (package + (name "r-gviz") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Gviz" version)) + (sha256 + (base32 + "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) + (properties `((upstream-name . "Gviz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Gviz") + (synopsis "Plotting data and annotation information along genomic coordinates") + (description + "Genomic data analyses requires integrated visualization of known genomic +information and new experimental data. Gviz uses the biomaRt and the +rtracklayer packages to perform live annotation queries to Ensembl and UCSC +and translates this to e.g. gene/transcript structures in viewports of the +grid graphics package. This results in genomic information plotted together +with your data.") + (license license:artistic2.0))) + +(define-public r-gwascat + (package + (name "r-gwascat") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gwascat" version)) + (sha256 + (base32 + "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-readr" ,r-readr) + ("r-s4vectors" ,r-s4vectors) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gwascat") + (synopsis "Tools for data in the EMBL-EBI GWAS catalog") + (description + "This package provides tools for representing and modeling data in the +EMBL-EBI GWAS catalog.") + (license license:artistic2.0))) + (define-public r-kegggraph (package (name "r-kegggraph") @@ -9267,6 +9584,68 @@ maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.") (license license:gpl2+))) +(define-public r-ldblock + (package + (name "r-ldblock") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ldblock" version)) + (sha256 + (base32 + "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/ldblock") + (synopsis "Data structures for linkage disequilibrium measures in populations") + (description + "This package defines data structures for @dfn{linkage +disequilibrium} (LD) measures in populations. Its purpose is to simplify +handling of existing population-level data for the purpose of flexibly +defining LD blocks.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on r-snpstats, which is a +;; Bioconductor package. +(define-public r-ldheatmap + (package + (name "r-ldheatmap") + (version "1.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "LDheatmap" version)) + (sha256 + (base32 + "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) + (properties `((upstream-name . "LDheatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genetics" ,r-genetics) + ("r-rcpp" ,r-rcpp) + ("r-snpstats" ,r-snpstats))) + (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") + (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") + (description + "This package provides tools to produce a graphical display, as a heat +map, of measures of pairwise linkage disequilibria between SNPs. Users may +optionally include the physical locations or genetic map distances of each SNP +on the plot.") + (license license:gpl3))) + (define-public r-pathview (package (name "r-pathview") @@ -9300,3 +9679,52 @@ 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+))) + +(define-public r-snpstats + (package + (name "r-snpstats") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "snpStats" version)) + (sha256 + (base32 + "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) + (properties `((upstream-name . "snpStats"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-matrix" ,r-matrix) + ("r-survival" ,r-survival) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/snpStats") + (synopsis "Methods for SNP association studies") + (description + "This package provides classes and statistical methods for large +@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends +the earlier snpMatrix package, allowing for uncertainty in genotypes.") + (license license:gpl3))) + +(define-public r-sushi + (package + (name "r-sushi") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Sushi" version)) + (sha256 + (base32 + "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) + (properties `((upstream-name . "Sushi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biomart" ,r-biomart) + ("r-zoo" ,r-zoo))) + (home-page "https://bioconductor.org/packages/Sushi") + (synopsis "Tools for visualizing genomics data") + (description + "This package provides flexible, quantitative, and integrative genomic +visualizations for publication-quality multi-panel figures.") + (license license:gpl2+))) |