gnu: Add r-scater.

* gnu/packages/bioinformatics.scm (r-scater): New variable.

Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
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Ricardo Wurmus 2018-02-12 15:19:25 +01:00
parent 6fb1dc17a3
commit 658ab21d2e
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1 changed files with 45 additions and 1 deletions

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@ -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