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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;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
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;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
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;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
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;;;
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@ -10538,6 +10538,50 @@ factors for each cell, along with the usual metadata for genes and
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libraries.")
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(license license:gpl3)))
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(define-public r-scater
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(package
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(name "r-scater")
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(version "1.6.2")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "scater" version))
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(sha256
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(base32
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"0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-beachmat" ,r-beachmat)
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("r-biobase" ,r-biobase)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biomart" ,r-biomart)
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("r-data-table" ,r-data-table)
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("r-dplyr" ,r-dplyr)
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("r-edger" ,r-edger)
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("r-ggbeeswarm" ,r-ggbeeswarm)
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("r-ggplot2" ,r-ggplot2)
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("r-limma" ,r-limma)
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("r-matrix" ,r-matrix)
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("r-matrixstats" ,r-matrixstats)
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("r-plyr" ,r-plyr)
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("r-rcpp" ,r-rcpp)
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("r-reshape2" ,r-reshape2)
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("r-rhdf5" ,r-rhdf5)
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("r-rhdf5lib" ,r-rhdf5lib)
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("r-rjson" ,r-rjson)
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("r-s4vectors" ,r-s4vectors)
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("r-shiny" ,r-shiny)
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("r-shinydashboard" ,r-shinydashboard)
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("r-singlecellexperiment" ,r-singlecellexperiment)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-tximport" ,r-tximport)
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("r-viridis" ,r-viridis)))
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(home-page "https://github.com/davismcc/scater")
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(synopsis "Single-cell analysis toolkit for gene expression data in R")
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(description "This package provides a collection of tools for doing
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various analyses of single-cell RNA-seq gene expression data, with a focus on
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quality control.")
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(license license:gpl2+)))
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(define htslib-for-sambamba
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(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
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(package
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