51 lines
2.6 KiB
Python
51 lines
2.6 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class RSva(RPackage):
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"""Surrogate Variable Analysis.
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The sva package contains functions for removing batch effects and other
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unwanted variation in high-throughput experiment. Specifically, the sva
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package contains functions for the identifying and building surrogate
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variables for high-dimensional data sets. Surrogate variables are
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covariates constructed directly from high-dimensional data (like gene
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expression/RNA sequencing/methylation/brain imaging data) that can be
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used in subsequent analyses to adjust for unknown, unmodeled, or latent
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sources of noise. The sva package can be used to remove artifacts in
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three ways: (1) identifying and estimating surrogate variables for
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unknown sources of variation in high-throughput experiments (Leek and
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Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch
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effects using ComBat (Johnson et al. 2007 Biostatistics) and (3)
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removing batch effects with known control probes (Leek 2014 biorXiv).
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Removing batch effects and using surrogate variables in differential
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expression analysis have been shown to reduce dependence, stabilize
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error rate estimates, and improve reproducibility, see (Leek and Storey
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2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews
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Genetics)."""
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bioc = "sva"
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version("3.48.0", commit="f1657af586d402598df71ade10dfeb28aa28b5c4")
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version("3.46.0", commit="4aac49cf806f05bb98e08a6be539adebbecbfdb2")
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version("3.44.0", commit="45ab2c1d6643bcda4de2d95a81b9b28d33a1a8a1")
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version("3.42.0", commit="54c843cc46437be233ecb43b6aa868e968d71138")
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version("3.38.0", commit="5ded8ba649200ec4829051f86a59e1a2548a7ab8")
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version("3.32.1", commit="1b8286734d00533b49d9f1456b6523cc778bb744")
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version("3.30.1", commit="fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c")
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version("3.28.0", commit="dd4937229dbccd2f383a04d5237fe147a884728d")
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version("3.26.0", commit="3cc5e75413c35ed5511892f5c36a8b5cb454937e")
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version("3.24.4", commit="ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73")
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depends_on("r@3.2:", type=("build", "run"))
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depends_on("r-mgcv", type=("build", "run"))
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depends_on("r-genefilter", type=("build", "run"))
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depends_on("r-biocparallel", type=("build", "run"))
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depends_on("r-matrixstats", type=("build", "run"))
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depends_on("r-limma", type=("build", "run"))
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depends_on("r-edger", type=("build", "run"), when="@3.38.0:")
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