diff --git a/var/spack/repos/builtin/packages/r-dexseq/package.py b/var/spack/repos/builtin/packages/r-dexseq/package.py new file mode 100644 index 0000000000..f3f584c8e3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dexseq/package.py @@ -0,0 +1,42 @@ +# Copyright 2013-2021 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 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('1.36.0', commit='f0a361af6954fcc2abb2db801c26e303570669b2') + + depends_on('r-stringr', type=('build', 'run')) + depends_on('r-geneplotter', type=('build', 'run')) + depends_on('r-genefilter', 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-rsamtools', type=('build', 'run')) + depends_on('r-statmod', type=('build', 'run')) + 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-annotationdbi', type=('build', 'run')) + depends_on('r-rcolorbrewer', type=('build', 'run')) + depends_on('r-s4vectors@0.23.18:', type=('build', 'run'))