49 lines
2.4 KiB
Python
49 lines
2.4 KiB
Python
# Copyright 2013-2023 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 RMethylumi(RPackage):
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"""Handle Illumina methylation data.
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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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bioc = "methylumi"
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version("2.44.0", commit="8f1f1f944993800da2776cb3240b4482c09429ad")
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version("2.42.0", commit="73e9c7fe1252c4ca20dc7b4e58decf04bf22d5e0")
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version("2.40.1", commit="211039225ca6fca9af75b8266f656161912ce10f")
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version("2.36.0", commit="5fb0b609f9c9181ac99f902745958774e5489606")
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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-s4vectors", type=("build", "run"), when="@2.36.0:")
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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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depends_on("r-genomicfeatures", type=("build", "run"), when="@2.40.1:")
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