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
35 lines
1.6 KiB
Python
35 lines
1.6 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 RVsn(RPackage):
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"""The package implements a method for normalising microarray intensities,
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and works for single- and multiple-color arrays. It can also be used
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for data from other technologies, as long as they have similar format.
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The method uses a robust variant of the maximum-likelihood estimator
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for an additive-multiplicative error model and affine calibration. The
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model incorporates data calibration step (a.k.a. normalization), a
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model for the dependence of the variance on the mean intensity and a
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variance stabilizing data transformation. Differences between
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transformed intensities are analogous to "normalized log-ratios".
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However, in contrast to the latter, their variance is independent of
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the mean, and they are usually more sensitive and specific in detecting
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differential transcription."""
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homepage = "https://www.bioconductor.org/packages/vsn/"
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git = "https://git.bioconductor.org/packages/vsn.git"
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version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
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depends_on('r-biobase', type=('build', 'run'))
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depends_on('r-affy', type=('build', 'run'))
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depends_on('r-limma', type=('build', 'run'))
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depends_on('r-lattice', type=('build', 'run'))
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depends_on('r-ggplot2', type=('build', 'run'))
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depends_on('r-hexbin', type=('build', 'run'))
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depends_on('r@3.4.0:3.4.9', when='@3.44.0')
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