41 lines
1.8 KiB
Python
41 lines
1.8 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 RDmrcate(RPackage):
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"""Methylation array and sequencing spatial analysis methods.
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De novo identification and extraction of differentially methylated regions
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(DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS)
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and Illumina Infinium Array (450K and EPIC) data. Provides functionality
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for filtering probes possibly confounded by SNPs and cross-hybridisation.
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Includes GRanges generation and plotting functions."""
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bioc = "DMRcate"
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version("2.12.0", commit="560dd5067b05715631739d0fb58ef9cebdbf7078")
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version("2.10.0", commit="81e83701da5c55ac83d0e0b5e640a9d431f09551")
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version("2.8.5", commit="c65dc79a33a047c10932a98b3383709a6bcb8903")
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version("2.4.1", commit="bc6242a0291a9b997872f575a4417d38550c9550")
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depends_on("r@3.6.0:", type=("build", "run"))
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depends_on("r@4.0.0:", type=("build", "run"), when="@2.8.5:")
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depends_on("r-experimenthub", type=("build", "run"))
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depends_on("r-bsseq", type=("build", "run"))
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depends_on("r-genomeinfodb", type=("build", "run"))
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depends_on("r-limma", type=("build", "run"))
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depends_on("r-edger", type=("build", "run"))
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depends_on("r-dss", type=("build", "run"))
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depends_on("r-minfi", type=("build", "run"))
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depends_on("r-missmethyl", type=("build", "run"))
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depends_on("r-genomicranges", type=("build", "run"))
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depends_on("r-plyr", type=("build", "run"))
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depends_on("r-gviz", type=("build", "run"))
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depends_on("r-iranges", type=("build", "run"))
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depends_on("r-s4vectors", type=("build", "run"))
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depends_on("r-summarizedexperiment", type=("build", "run"))
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