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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RVsn(RPackage):
"""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."""
homepage = "https://www.bioconductor.org/packages/vsn/"
url = "https://git.bioconductor.org/packages/vsn"
version('3.44.0', git='https://git.bioconductor.org/packages/vsn', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
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'))
depends_on('r@3.4.0:3.4.9', when='@3.44.0')
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