39 lines
1.9 KiB
Python
39 lines
1.9 KiB
Python
# Copyright Spack Project Developers. See 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.package 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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bioc = "sSeq"
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version("1.38.0", commit="09242bb94d72ff13e3f18c3588934149f27ac374")
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version("1.36.0", commit="0345ac579c4bdcc9c42c24831ad86fc6225c5cb9")
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version("1.34.0", commit="882bea1664f55d85550a7185cbd4a0108c35df36")
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version("1.32.0", commit="c0d3c305755d888f64d334a4ab5fa54c623054cf")
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version("1.28.0", commit="401f6805628bdf6579cc0e643b7ed54319f024be")
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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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