eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
33 lines
1.5 KiB
Python
33 lines
1.5 KiB
Python
# Copyright 2013-2018 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 RAldex2(RPackage):
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"""A differential abundance analysis for the comparison of
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two or more conditions. For example, single-organism and
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meta-RNA-seq high-throughput sequencing assays, or of
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selected and unselected values from in-vitro sequence selections.
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Uses a Dirichlet-multinomial model to infer abundance from counts,
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that has been optimized for three or more experimental replicates.
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Infers sampling variation and calculates the expected false
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discovery rate given the biological and sampling variation
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using the Wilcox rank test or Welches t-test (aldex.ttest) or
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the glm and Kruskal Wallis tests (aldex.glm). Reports both P
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and fdr values calculated by the Benjamini Hochberg correction."""
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homepage = "http://bioconductor.org/packages/ALDEx2/"
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git = "https://git.bioconductor.org/packages/ALDEx2.git"
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version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
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depends_on('r@3.4.0:3.4.9', when='@1.8.0')
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depends_on('r-s4vectors', type=('build', 'run'))
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depends_on('r-iranges', 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-biocparallel', type=('build', 'run'))
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