r-ruv: new package (#23113)

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
new file mode 100644
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+++ 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'))