@@ 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