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# Copyright 2013-2023 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 RDexseq(RPackage):
"""Inference of differential exon usage in RNA-Seq.
The package is focused on finding differential exon usage using RNA-seq
exon counts between samples with different experimental designs. It
provides functions that allows the user to make the necessary
statistical tests based on a model that uses the negative binomial
distribution to estimate the variance between biological replicates
and generalized linear models for testing. The package also provides
functions for the visualization and exploration of the results."""
bioc = "DEXSeq"
maintainers("dorton21")
version("1.46.0", commit="074c0bf6776eea69e58a788a0f6904dd632a1b74")
version("1.44.0", commit="9660d7372d5ced1a7e324ed9a61b935023b7d135")
version("1.42.0", commit="d91de62a27d0cab2ef12ef1a5f23dc2f7a0cfadd")
version("1.40.0", commit="7d2d639b3a157e443058fc557132cd2629bb36f3")
version("1.36.0", commit="f0a361af6954fcc2abb2db801c26e303570669b2")
depends_on("r-biocparallel", type=("build", "run"))
depends_on("r-biobase", type=("build", "run"))
depends_on("r-summarizedexperiment", type=("build", "run"))
depends_on("r-iranges@2.5.17:", type=("build", "run"))
depends_on("r-genomicranges@1.23.7:", type=("build", "run"))
depends_on("r-deseq2@1.9.11:", type=("build", "run"))
depends_on("r-deseq2@1.39.6:", type=("build", "run"), when="@1.46.0:")
depends_on("r-annotationdbi", type=("build", "run"))
depends_on("r-rcolorbrewer", type=("build", "run"))
depends_on("r-s4vectors@0.23.18:", type=("build", "run"))
depends_on("r-biocgenerics", type=("build", "run"))
depends_on("r-biomart", type=("build", "run"))
depends_on("r-hwriter", type=("build", "run"))
depends_on("r-stringr", type=("build", "run"))
depends_on("r-rsamtools", type=("build", "run"))
depends_on("r-statmod", type=("build", "run"))
depends_on("r-geneplotter", type=("build", "run"))
depends_on("r-genefilter", type=("build", "run"))
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