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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-02-12 15:19:25 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-02-12 15:29:43 +0100 |
| commit | 658ab21d2e16bda0a8c3cfc8f4cc4715628b6247 (patch) | |
| tree | b0dd2ee97b1205182015f304ff5f21ba2730828b /gnu/packages/bioinformatics.scm | |
| parent | 6fb1dc17a3898eb04178235d86aa0da480523d34 (diff) | |
| download | patches-658ab21d2e16bda0a8c3cfc8f4cc4715628b6247.tar patches-658ab21d2e16bda0a8c3cfc8f4cc4715628b6247.tar.gz | |
gnu: Add r-scater.
* gnu/packages/bioinformatics.scm (r-scater): New variable.
Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 45 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 912769efb7..16bb1c0f8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> -;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> +;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; @@ -10538,6 +10538,50 @@ factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) +(define-public r-scater + (package + (name "r-scater") + (version "1.6.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scater" version)) + (sha256 + (base32 + "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tximport" ,r-tximport) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/davismcc/scater") + (synopsis "Single-cell analysis toolkit for gene expression data in R") + (description "This package provides a collection of tools for doing +various analyses of single-cell RNA-seq gene expression data, with a focus on +quality control.") + (license license:gpl2+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package |