54 lines
2.6 KiB
Python
54 lines
2.6 KiB
Python
##############################################################################
|
|
# 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 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://git.bioconductor.org/packages/ABAEnrichment"
|
|
|
|
version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
|
|
|
|
depends_on('r@3.4.0:3.4.9', when='@1.6.0')
|
|
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'))
|