52 lines
2.6 KiB
Python
52 lines
2.6 KiB
Python
# Copyright Spack Project Developers. See 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 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("1.34.0", commit="57db57c48ab79c36eb89726afc2833a981cbaf3d")
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version("1.32.0", commit="969b892e400b9821398099bcea46f2d0431daedf")
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version("1.30.0", commit="734846653f332f10e557b87aca4cb5d100b62469")
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version("1.28.0", commit="6a36aee28837736291ac630c1da3909f0e9c8d6a")
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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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