36 lines
1.7 KiB
Python
36 lines
1.7 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class RSseq(RPackage):
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"""Shrinkage estimation of dispersion in Negative Binomial models for RNA-
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seq experiments with small sample size.
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The purpose of this package is to discover the genes that are
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differentially expressed between two conditions in RNA-seq experiments.
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Gene expression is measured in counts of transcripts and modeled with
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the Negative Binomial (NB) distribution using a shrinkage approach for
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dispersion estimation. The method of moment (MM) estimates for
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dispersion are shrunk towards an estimated target, which minimizes the
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average squared difference between the shrinkage estimates and the
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initial estimates. The exact per-gene probability under the NB model is
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calculated, and used to test the hypothesis that the expected expression
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of a gene in two conditions identically follow a NB distribution."""
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homepage = "https://bioconductor.org/packages/sSeq"
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git = "https://git.bioconductor.org/packages/sSeq.git"
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version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc')
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version('1.20.1', commit='91f31440323612cb04beb44404ab0a1bcb3ad87d')
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version('1.18.0', commit='1f65e5a55ce0d51672b785450031872e6db5ca0f')
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version('1.16.0', commit='b7f2b99dbd4a12ee9d18b0ec9898f13f1038479e')
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version('1.14.0', commit='20ccffeb60196914975aa1feef902ddba659c571')
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depends_on('r@3.0:', type=('build', 'run'))
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depends_on('r-catools', type=('build', 'run'))
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depends_on('r-rcolorbrewer', type=('build', 'run'))
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