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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDeseq2(RPackage):
"""Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution."""
homepage = "https://www.bioconductor.org/packages/DESeq2/"
git = "https://git.bioconductor.org/packages/DESeq2.git"
version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5')
depends_on("r-rcpparmadillo", type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-geneplotter', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run'))
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