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| -rw-r--r-- | var/spack/repos/builtin/packages/r-champ/package.py | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py new file mode 100644 index 0000000000..478030a7c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-champ/package.py @@ -0,0 +1,60 @@ +# Copyright 2013-2021 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 import * + + +class RChamp(RPackage): + """Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and + EPIC: + + The package includes quality control metrics, a selection of + normalization methods and novel methods to identify differentially + methylated regions and to highlight copy number alterations.""" + + bioc = "ChAMP" + + version('2.20.1', commit='99ea0463bce59f5b06bcc91f479dcd4065074896') + + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-minfi', type=('build', 'run')) + depends_on('r-champdata@2.6.0:', type=('build', 'run')) + depends_on('r-dmrcate', type=('build', 'run')) + depends_on('r-illumina450probevariants-db', type=('build', 'run')) + depends_on('r-illuminahumanmethylationepicmanifest', type=('build', 'run')) + depends_on('r-dt', type=('build', 'run')) + depends_on('r-rpmm', type=('build', 'run')) + depends_on('r-prettydoc', type=('build', 'run')) + depends_on('r-hmisc', type=('build', 'run')) + depends_on('r-globaltest', type=('build', 'run')) + depends_on('r-sva', type=('build', 'run')) + depends_on('r-illuminaio', type=('build', 'run')) + depends_on('r-rmarkdown', type=('build', 'run')) + depends_on('r-illuminahumanmethylation450kmanifest', type=('build', 'run')) + depends_on('r-illuminahumanmethylationepicanno-ilm10b4-hg19', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-dnacopy', type=('build', 'run')) + depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-impute', type=('build', 'run')) + depends_on('r-marray', type=('build', 'run')) + depends_on('r-watermelon', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-goseq', type=('build', 'run')) + depends_on('r-missmethyl', type=('build', 'run')) + depends_on('r-kpmt', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-isva', type=('build', 'run')) + depends_on('r-doparallel', type=('build', 'run')) + depends_on('r-bumphunter', type=('build', 'run')) + depends_on('r-quadprog', type=('build', 'run')) + depends_on('r-shiny', type=('build', 'run')) + depends_on('r-shinythemes', type=('build', 'run')) + depends_on('r-plotly@4.5.6:', type=('build', 'run')) + depends_on('r-rcolorbrewer', type=('build', 'run')) + depends_on('r-dendextend', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-combinat', type=('build', 'run')) |