diff options
author | lingnanyuan <1297162327@qq.com> | 2017-10-05 09:57:42 -0500 |
---|---|---|
committer | Christoph Junghans <christoph.junghans@gmail.com> | 2017-10-05 08:57:42 -0600 |
commit | f54e30b0655edfc8147af8ed238769ab49fc4cd7 (patch) | |
tree | 1afdc99ea67e7088fb805121667b0070cb7e8e9b /var | |
parent | 44653dc7aaa02bf1ddd6436903e999eabf651051 (diff) | |
download | spack-f54e30b0655edfc8147af8ed238769ab49fc4cd7.tar.gz spack-f54e30b0655edfc8147af8ed238769ab49fc4cd7.tar.bz2 spack-f54e30b0655edfc8147af8ed238769ab49fc4cd7.tar.xz spack-f54e30b0655edfc8147af8ed238769ab49fc4cd7.zip |
r-abaenrichment: Create new package. (#5612)
Diffstat (limited to 'var')
-rw-r--r-- | var/spack/repos/builtin/packages/r-abaenrichment/package.py | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py new file mode 100644 index 0000000000..6029c185d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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/llnl/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 RAbaenrichment(RPackage): + """The package ABAEnrichment is designed to test for enrichment + of user defined candidate genes in the set of expressed genes in + different human brain regions. The core function 'aba_enrich' + integrates the expression of the candidate gene set (averaged + across donors) and the structural information of the brain using + an ontology, both provided by the Allen Brain Atlas project. + 'aba_enrich' interfaces the ontology enrichment software FUNC to + perform the statistical analyses. Additional functions provided + in this package like 'get_expression' and 'plot_expression' + facilitate exploring the expression data. From version 1.3.5 + onwards genomic regions can be provided as input, too; and from + version 1.5.9 onwards the function 'get_annotated_genes' offers + an easy way to obtain annotations of genes to enriched or + user-defined brain regions.""" + + homepage = "https://bioconductor.org/packages/ABAEnrichment/" + url = "https://bioconductor.org/packages/release/bioc/src/contrib/ABAEnrichment_1.6.0.tar.gz" + + version('1.6.0', '810eb4ee9ce2a5049babbb174dc8d588') + + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-gplots', type=('build', 'run')) + depends_on('r-gtools', type=('build', 'run')) + depends_on('r-abadata', type=('build', 'run')) |