diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/r-gofuncr/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/r-gofuncr/package.py | 62 |
1 files changed, 31 insertions, 31 deletions
diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py index 62c0d992b2..e87b20fd2a 100644 --- a/var/spack/repos/builtin/packages/r-gofuncr/package.py +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -9,38 +9,38 @@ from spack.package import * class RGofuncr(RPackage): """Gene ontology enrichment using FUNC. - GOfuncR performs a gene ontology enrichment analysis based on the - ontology enrichment software FUNC. GO-annotations are obtained from - OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph - is included in the package and updated regularly (27-Mar-2019). GOfuncR - provides the standard candidate vs. background enrichment analysis using - the hypergeometric test, as well as three additional tests: (i) the - Wilcoxon rank-sum test that is used when genes are ranked, (ii) a - binomial test that is used when genes are associated with two counts and - (iii) a Chi-square or Fisher's exact test that is used in cases when - genes are associated with four counts. To correct for multiple testing - and interdependency of the tests, family-wise error rates are computed - based on random permutations of the gene-associated variables. GOfuncR - also provides tools for exploring the ontology graph and the - annotations, and options to take gene-length or spatial clustering of - genes into account. It is also possible to provide custom gene - coordinates, annotations and ontologies.""" + GOfuncR performs a gene ontology enrichment analysis based on the + ontology enrichment software FUNC. GO-annotations are obtained from + OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph + is included in the package and updated regularly (27-Mar-2019). GOfuncR + provides the standard candidate vs. background enrichment analysis using + the hypergeometric test, as well as three additional tests: (i) the + Wilcoxon rank-sum test that is used when genes are ranked, (ii) a + binomial test that is used when genes are associated with two counts and + (iii) a Chi-square or Fisher's exact test that is used in cases when + genes are associated with four counts. To correct for multiple testing + and interdependency of the tests, family-wise error rates are computed + based on random permutations of the gene-associated variables. GOfuncR + also provides tools for exploring the ontology graph and the + annotations, and options to take gene-length or spatial clustering of + genes into account. It is also possible to provide custom gene + coordinates, annotations and ontologies.""" bioc = "GOfuncR" - version('1.16.0', commit='603fc79e13b58ec4612b6092f37d2450078dbfe1') - version('1.14.0', commit='b3d445acf95851241d1fdb673d108ee115bdc17b') - version('1.10.0', commit='51b01a2b9afa03fde2e1628036096cbeafaa2ef4') - version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709') - version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded') - version('1.0.0', commit='becd4ddde085c5477042adb856e7a4f40dbd648e') + version("1.16.0", commit="603fc79e13b58ec4612b6092f37d2450078dbfe1") + version("1.14.0", commit="b3d445acf95851241d1fdb673d108ee115bdc17b") + version("1.10.0", commit="51b01a2b9afa03fde2e1628036096cbeafaa2ef4") + version("1.4.0", commit="2f633dc28e3faeddc5346fcdcadf1c29e3fcf709") + version("1.2.0", commit="140a3cea4fe34d32fef9be756f85e337ce3deded") + version("1.0.0", commit="becd4ddde085c5477042adb856e7a4f40dbd648e") - depends_on('r+X', type=('build', 'run')) - depends_on('r@3.4:', type=('build', 'run')) - depends_on('r-vioplot@0.2:', type=('build', 'run')) - depends_on('r-rcpp@0.11.5:', type=('build', 'run')) - depends_on('r-mapplots@1.5:', type=('build', 'run')) - depends_on('r-gtools@3.5.0:', type=('build', 'run')) - depends_on('r-genomicranges@1.28.4:', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run'), when='@1.2.0:') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on("r+X", type=("build", "run")) + depends_on("r@3.4:", type=("build", "run")) + depends_on("r-vioplot@0.2:", type=("build", "run")) + depends_on("r-rcpp@0.11.5:", type=("build", "run")) + depends_on("r-mapplots@1.5:", type=("build", "run")) + depends_on("r-gtools@3.5.0:", type=("build", "run")) + depends_on("r-genomicranges@1.28.4:", type=("build", "run")) + depends_on("r-iranges", type=("build", "run"), when="@1.2.0:") + depends_on("r-annotationdbi", type=("build", "run")) |