28 lines
1.2 KiB
Python
28 lines
1.2 KiB
Python
# Copyright 2013-2021 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 RExomecopy(RPackage):
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"""Copy number variant detection from exome sequencing read depth
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Detection of copy number variants (CNV) from exome sequencing samples,
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including unpaired samples. The package implements a hidden Markov model
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which uses positional covariates, such as background read depth and
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GC-content, to simultaneously normalize and segment the samples into
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regions of constant copy count."""
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homepage = "http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
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git = "https://git.bioconductor.org/packages/exomeCopy"
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version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26')
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version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')
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depends_on('r-iranges@2.5.27:', type=('build', 'run'))
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depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
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depends_on('r-rsamtools', type=('build', 'run'))
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depends_on('r-genomeinfodb', type=('build', 'run'))
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