43 lines
2.2 KiB
Python
43 lines
2.2 KiB
Python
# Copyright 2013-2022 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 RAldex2(RPackage):
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"""Analysis Of Differential Abundance Taking Sample Variation Into Account.
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A differential abundance analysis for the comparison of two or more
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conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-
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seq assays as well as selected and unselected values from in-vitro
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sequence selections. Uses a Dirichlet-multinomial model to infer
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abundance from counts, optimized for three or more experimental
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replicates. The method infers biological and sampling variation to
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calculate the expected false discovery rate, given the variation, based
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on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a
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Kruskal-Wallis test (via aldex.kw), a generalized linear model (via
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aldex.glm), or a correlation test (via aldex.corr). All tests report
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p-values and Benjamini-Hochberg corrected p-values."""
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bioc = "ALDEx2"
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version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6")
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version("1.26.0", commit="0876a2eac08d3f1c01df7414d97d391c80182ada")
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version("1.22.0", commit="ac7f0ab3f094ec52713da7620a27058b14c7181d")
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version("1.16.0", commit="bd698a896a5bea91187e3060e56a147bad1d586f")
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version("1.14.1", commit="a8b970c594a00a37c064227bf312d5f89dccabe8")
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version("1.12.0", commit="9efde428d22a0be1fe7b6655d45ddce8fcded180")
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version("1.10.0", commit="e43f99e4009ad4d5ed200cc8a19faf7091c0c98a")
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version("1.8.0", commit="24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1")
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depends_on("r-zcompositions", type=("build", "run"), when="@1.22.0:")
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depends_on("r-rfast", type=("build", "run"), when="@1.26.0:")
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depends_on("r-biocparallel", type=("build", "run"))
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depends_on("r-genomicranges", 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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depends_on("r-multtest", type=("build", "run"), when="@1.10.0:")
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