8aa1eba2e0
This PR creates the r-watermelon package, along with dependencies. - new package: r-fdb-infiniummethylation-hg19 - new package: r-illuminahumanmethylation450kanno-ilmn12-hg19 - new package: r-lumi - new package: r-methylumi - new package: r-roc - new package: r-txdb-hsapiens-ucsc-hg19-knowngene - updated package: r-matrixstats, new version needed as a dependency
42 lines
2.0 KiB
Python
42 lines
2.0 KiB
Python
# Copyright 2013-2020 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 RMethylumi(RPackage):
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"""This package provides classes for holding and manipulating Illumina
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methylation data. Based on eSet, it can contain MIAME information, sample
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information, feature information, and multiple matrices of data. An
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"intelligent" import function, methylumiR can read the Illumina text files
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and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files
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from HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
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background correction, and quality control features for GoldenGate,
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Infinium, and Infinium HD arrays are also included."""
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homepage = "https://bioconductor.org/packages/release/bioc/html/methylumi.html"
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git = "https://git.bioconductor.org/packages/methylumi"
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version('2.32.0', commit='e2a29c1b214c0d43c7325d176f9ce41dcf8e2f9d')
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depends_on('r@2.13:', type=('build', 'run'))
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depends_on('r-biobase', type=('build', 'run'))
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depends_on('r-scales', type=('build', 'run'))
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depends_on('r-reshape2', type=('build', 'run'))
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depends_on('r-ggplot2', type=('build', 'run'))
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depends_on('r-matrixstats', type=('build', 'run'))
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depends_on('r-fdb-infiniummethylation-hg19@2.2.0:', type=('build', 'run'))
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depends_on('r-minfi', type=('build', 'run'))
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depends_on('r-biocgenerics', type=('build', 'run'))
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depends_on('r-iranges', type=('build', 'run'))
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depends_on('r-genomeinfodb', type=('build', 'run'))
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depends_on('r-genomicranges', type=('build', 'run'))
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depends_on('r-summarizedexperiment', type=('build', 'run'))
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depends_on('r-lattice', type=('build', 'run'))
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depends_on('r-annotate', type=('build', 'run'))
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depends_on('r-genefilter', type=('build', 'run'))
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depends_on('r-annotationdbi', type=('build', 'run'))
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depends_on('r-illuminaio', type=('build', 'run'))
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