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| -rw-r--r-- | gnu/packages/bioconductor.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a98971e294..a4d97fad65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9006,6 +9006,53 @@ provides a wrapper of de novo motif discovery software.") This package wraps C++ code from the MOODS motif calling library.") (license license:gpl3))) +(define-public r-chromvar + (package + (name "r-chromvar") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chromVAR" version)) + (sha256 + (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) + (properties `((upstream-name . "chromVAR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dt" ,r-dt) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-miniui" ,r-miniui) + ("r-nabor" ,r-nabor) + ("r-plotly" ,r-plotly) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsamtools" ,r-rsamtools) + ("r-rtsne" ,r-rtsne) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tfbstools" ,r-tfbstools))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") + (synopsis "Determine chromatin variation across regions") + (description + "This package @code{r-chromvar} determines variation in chromatin +accessibility across sets of annotations or peaks. @code{r-chromvar} is +designed primarily for single-cell or sparse chromatin accessibility data like +single cell assay for transposase-accessible chromatin using +sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease +sequence (@code{DNAse-seq}) experiments.") + (license license:expat))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") |