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authorGlenn Johnson <glenn-johnson@uiowa.edu>2021-04-20 04:09:48 -0500
committerGitHub <noreply@github.com>2021-04-20 11:09:48 +0200
commit37263d7b717aee35e25ce5401655404256b97da4 (patch)
tree63cf9124f994bac312c34831c828a917f80699ee
parent11c529fddcd57b25d960ccd26d319d479521780c (diff)
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r-ruv: new package (#23113)
-rw-r--r--var/spack/repos/builtin/packages/r-ruv/package.py32
1 files changed, 32 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-ruv/package.py b/var/spack/repos/builtin/packages/r-ruv/package.py
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+# 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 RRuv(RPackage):
+ """Detect and Remove Unwanted Variation using Negative Controls:
+
+ Implements the 'RUV' (Remove Unwanted Variation) algorithms. These
+ algorithms attempt to adjust for systematic errors of unknown origin in
+ high-dimensional data. The algorithms were originally developed for use
+ with genomic data, especially microarray data, but may be useful with other
+ types of high-dimensional data as well. These algorithms were proposed in
+ Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch,
+ Jacob and Speed (2013), and Molania, et. al. (2019)
+ <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set
+ of negative control variables, as described in the references. The
+ algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv',
+ 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting
+ algorithms."""
+
+ homepage = "http://www-personal.umich.edu/~johanngb/ruv/"
+ cran = "ruv"
+
+ version('0.9.7.1', sha256='a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8')
+
+ depends_on('r-ggplot2', type=('build', 'run'))
+ depends_on('r-scales', type=('build', 'run'))
+ depends_on('r-gridextra', type=('build', 'run'))