49 lines
2.4 KiB
Python
49 lines
2.4 KiB
Python
# Copyright 2013-2021 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 import *
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class RMissmethyl(RPackage):
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"""Analysing Illumina HumanMethylation BeadChip Data:
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Normalisation, testing for differential variability and differential
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methylation and gene set testing for data from Illumina's Infinium
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HumanMethylation arrays. The normalisation procedure is subset-quantile
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within-array normalisation (SWAN), which allows Infinium I and II type
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probes on a single array to be normalised together. The test for
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differential variability is based on an empirical Bayes version of Levene's
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test. Differential methylation testing is performed using RUV, which can
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adjust for systematic errors of unknown origin in high-dimensional data by
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using negative control probes. Gene ontology analysis is performed by
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taking into account the number of probes per gene on the array, as well as
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taking into account multi-gene associated probes."""
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bioc = "missMethyl"
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version('1.24.0', commit='f6c86048911dc0e302fb593b7d0623f6e77ac332')
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depends_on('r@3.6.0:', type=('build', 'run'))
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depends_on('r-illuminahumanmethylation450kanno-ilmn12-hg19', type=('build', 'run'))
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depends_on('r-illuminahumanmethylationepicanno-ilm10b4-hg19', type=('build', 'run'))
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depends_on('r-annotationdbi', type=('build', 'run'))
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depends_on('r-biasedurn', type=('build', 'run'))
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depends_on('r-biobase', type=('build', 'run'))
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depends_on('r-biocgenerics', type=('build', 'run'))
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depends_on('r-genomicranges', type=('build', 'run'))
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depends_on('r-go-db', type=('build', 'run'))
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depends_on('r-illuminahumanmethylation450kmanifest', type=('build', 'run'))
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depends_on('r-illuminahumanmethylationepicmanifest', type=('build', 'run'))
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depends_on('r-iranges', type=('build', 'run'))
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depends_on('r-limma', type=('build', 'run'))
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depends_on('r-methylumi', type=('build', 'run'))
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depends_on('r-minfi', type=('build', 'run'))
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depends_on('r-org-hs-eg-db', type=('build', 'run'))
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depends_on('r-ruv', type=('build', 'run'))
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depends_on('r-s4vectors', type=('build', 'run'))
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depends_on('r-statmod', type=('build', 'run'))
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depends_on('r-stringr', type=('build', 'run'))
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depends_on('r-summarizedexperiment', type=('build', 'run'))
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