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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 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."""
cran = "ruv"
license("GPL-2.0-or-later")
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"))
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