New Package r-dexseq (#23457)

1 files changed, 42 insertions, 0 deletions

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'))