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# Copyright 2013-2022 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.package import *
class REdger(RPackage):
"""Empirical Analysis of Digital Gene Expression Data in R.
Differential expression analysis of RNA-seq expression profiles with
biological replication. Implements a range of statistical methodology
based on the negative binomial distributions, including empirical Bayes
estimation, exact tests, generalized linear models and quasi-likelihood
tests. As well as RNA-seq, it be applied to differential signal analysis
of other types of genomic data that produce counts, including ChIP-seq,
Bisulfite-seq, SAGE and CAGE."""
bioc = "edgeR"
version('3.38.1', commit='e58bf52f34ec451096f593126922ad7e5d517f7e')
version('3.36.0', commit='c7db03addfc42138a1901834409c02da9d873026')
version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a')
version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d')
version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902')
version('3.20.9', commit='acbcbbee939f399673678653678cd9cb4917c4dc')
version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@3.26.8:')
depends_on('r-limma', type=('build', 'run'))
depends_on('r-limma@3.34.5:', type=('build', 'run'), when='@3.20.9:')
depends_on('r-limma@3.41.5:', type=('build', 'run'), when='@3.32.1:')
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'), when='@3.20.9:')
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