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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 RSva(RPackage):
"""Surrogate Variable Analysis.
The sva package contains functions for removing batch effects and other
unwanted variation in high-throughput experiment. Specifically, the sva
package contains functions for the identifying and building surrogate
variables for high-dimensional data sets. Surrogate variables are
covariates constructed directly from high-dimensional data (like gene
expression/RNA sequencing/methylation/brain imaging data) that can be
used in subsequent analyses to adjust for unknown, unmodeled, or latent
sources of noise. The sva package can be used to remove artifacts in
three ways: (1) identifying and estimating surrogate variables for
unknown sources of variation in high-throughput experiments (Leek and
Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch
effects using ComBat (Johnson et al. 2007 Biostatistics) and (3)
removing batch effects with known control probes (Leek 2014 biorXiv).
Removing batch effects and using surrogate variables in differential
expression analysis have been shown to reduce dependence, stabilize
error rate estimates, and improve reproducibility, see (Leek and Storey
2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews
Genetics)."""
bioc = "sva"
version("3.48.0", commit="f1657af586d402598df71ade10dfeb28aa28b5c4")
version("3.46.0", commit="4aac49cf806f05bb98e08a6be539adebbecbfdb2")
version("3.44.0", commit="45ab2c1d6643bcda4de2d95a81b9b28d33a1a8a1")
version("3.42.0", commit="54c843cc46437be233ecb43b6aa868e968d71138")
version("3.38.0", commit="5ded8ba649200ec4829051f86a59e1a2548a7ab8")
version("3.32.1", commit="1b8286734d00533b49d9f1456b6523cc778bb744")
version("3.30.1", commit="fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c")
version("3.28.0", commit="dd4937229dbccd2f383a04d5237fe147a884728d")
version("3.26.0", commit="3cc5e75413c35ed5511892f5c36a8b5cb454937e")
version("3.24.4", commit="ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73")
depends_on("r@3.2:", type=("build", "run"))
depends_on("r-mgcv", type=("build", "run"))
depends_on("r-genefilter", type=("build", "run"))
depends_on("r-biocparallel", type=("build", "run"))
depends_on("r-matrixstats", type=("build", "run"))
depends_on("r-limma", type=("build", "run"))
depends_on("r-edger", type=("build", "run"), when="@3.38.0:")
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