gnu: Add r-snapatac.
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
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;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
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;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
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;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
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@ -7073,6 +7073,55 @@ (define-public infernal
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(supported-systems '("i686-linux" "x86_64-linux"))
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(license license:bsd-3)))
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(define-public r-snapatac
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(package
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(name "r-snapatac")
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(version "2.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/r3fang/SnapATAC")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av"))))
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(properties `((upstream-name . "SnapATAC")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bigmemory" ,r-bigmemory)
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("r-doparallel" ,r-doparallel)
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("r-dosnow" ,r-dosnow)
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("r-edger" ,r-edger)
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("r-foreach" ,r-foreach)
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("r-genomicranges" ,r-genomicranges)
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("r-igraph" ,r-igraph)
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("r-iranges" ,r-iranges)
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("r-irlba" ,r-irlba)
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("r-matrix" ,r-matrix)
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("r-plyr" ,r-plyr)
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("r-plot3d" ,r-plot3d)
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("r-rann" ,r-rann)
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("r-raster" ,r-raster)
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("r-rcolorbrewer" ,r-rcolorbrewer)
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("r-rhdf5" ,r-rhdf5)
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("r-rtsne" ,r-rtsne)
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("r-scales" ,r-scales)
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("r-viridis" ,r-viridis)))
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(home-page "https://github.com/r3fang/SnapATAC")
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(synopsis "Single nucleus analysis package for ATAC-Seq")
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(description
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"This package provides a fast and accurate analysis toolkit for single
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cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing).
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Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and
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reveal cell-type specific regulatory landscapes. However, the exceeding data
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sparsity has posed unique challenges for the data analysis. This package
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@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large-
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scale single cell ATAC-seq data which includes quality control, normalization,
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clustering analysis, differential analysis, motif inference and exploration of
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single cell ATAC-seq sequencing data.")
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(license license:gpl3)))
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(define-public r-scde
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(package
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(name "r-scde")
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