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# Copyright 2013-2018 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 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/"
git = "https://git.bioconductor.org/packages/ABAEnrichment.git"
version('1.6.0', 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'))
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