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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class RVsn(RPackage):
"""Variance stabilization and calibration for microarray data.
The package implements a method for normalising microarray intensities,
and works for single- and multiple-color arrays. It can also be used for
data from other technologies, as long as they have similar format. The
method uses a robust variant of the maximum-likelihood estimator for an
additive-multiplicative error model and affine calibration. The model
incorporates data calibration step (a.k.a. normalization), a model for
the dependence of the variance on the mean intensity and a variance
stabilizing data transformation. Differences between transformed
intensities are analogous to "normalized log-ratios". However, in
contrast to the latter, their variance is independent of the mean, and
they are usually more sensitive and specific in detecting differential
transcription."""
bioc = "vsn"
version('3.62.0', commit='6ae7f4e07ec1a5a9482cab892d98175983bfcd50')
version('3.58.0', commit='a451e6ae989623750feacf26d99683a7955adf85')
version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe')
version('3.50.0', commit='ad49fcc288c6065d0f04040acd688e7f0d7d927e')
version('3.48.1', commit='d57f64112004b1d73b3be625949830209de027eb')
version('3.46.0', commit='7ecfd20452348da27d6fcc052cbff2b9be777792')
version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.4.0:', type=('build', 'run'), when='@3.46.0:')
depends_on('r@4.0.0:', type=('build', 'run'), when='@3.62.0:')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-hexbin', type=('build', 'run'), when='@3.44.0:3.52.0')
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