diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/r-hexbin/package.py | 2 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-vsn/package.py | 53 |
2 files changed, 54 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index db51d68538..179914fca3 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -34,6 +34,6 @@ class RHexbin(RPackage): url = "https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/hexbin" - version('1.27.1', '7f380390c6511e97df10a810a3b3bb7c') + version('1.27.1', '7590ed158f8a57a71901bf6ca26f81be') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py new file mode 100644 index 0000000000..649f42ea5d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -0,0 +1,53 @@ +############################################################################## +# 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') |