45 lines
2.1 KiB
Python
45 lines
2.1 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 RLumi(RPackage):
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"""BeadArray Specific Methods for Illumina Methylation and Expression
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Microarrays.
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The lumi package provides an integrated solution for the Illumina
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microarray data analysis. It includes functions of Illumina BeadStudio
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(GenomeStudio) data input, quality control, BeadArray-specific variance
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stabilization, normalization and gene annotation at the probe level. It
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also includes the functions of processing Illumina methylation microarrays,
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especially Illumina Infinium methylation microarrays."""
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bioc = "lumi"
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version("2.52.0", commit="c6aa992a622dbaba4dae1b54c61835a37cce8e95")
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version("2.50.0", commit="8711b77a1b5b0a58770d25d3d079ad02208704f5")
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version("2.48.0", commit="1f988ffe04d2c0707b2202d2074d02b679a3204b")
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version("2.46.0", commit="a68932c17a61c99e58ebbd8008d078bec6adb4e7")
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version("2.42.0", commit="a643b3ba46fee951b8566ddd8216af7e6c92f6f6")
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version("2.38.0", commit="321d480d44ce9a0c02ce5af1bddc1f549abdea59")
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depends_on("r@2.10:", type=("build", "run"))
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depends_on("r-biobase@2.5.5:", type=("build", "run"))
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depends_on("r-affy@1.23.4:", type=("build", "run"))
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depends_on("r-methylumi@2.3.2:", type=("build", "run"))
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depends_on("r-genomicfeatures", type=("build", "run"))
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depends_on("r-genomicranges", type=("build", "run"))
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depends_on("r-annotate", type=("build", "run"))
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depends_on("r-lattice", type=("build", "run"))
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depends_on("r-mgcv@1.4-0:", type=("build", "run"))
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depends_on("r-nleqslv", type=("build", "run"))
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depends_on("r-kernsmooth", type=("build", "run"))
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depends_on("r-preprocesscore", type=("build", "run"))
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depends_on("r-rsqlite", type=("build", "run"))
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depends_on("r-dbi", type=("build", "run"))
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depends_on("r-annotationdbi", type=("build", "run"))
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depends_on("r-mass", type=("build", "run"))
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