- recipe bioconductor-gofuncr
Gene ontology enrichment using FUNC
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/GOfuncR.html
- License:
GPL (>= 2)
- Recipe:
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 (01-May-2021). 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.
- package bioconductor-gofuncr¶
-
- Versions:
1.18.0-0
,1.14.0-2
,1.14.0-1
,1.14.0-0
,1.12.0-0
,1.10.0-1
,1.10.0-0
,1.8.0-0
,1.6.0-0
,1.18.0-0
,1.14.0-2
,1.14.0-1
,1.14.0-0
,1.12.0-0
,1.10.0-1
,1.10.0-0
,1.8.0-0
,1.6.0-0
,1.4.0-1
,1.2.0-0
- Depends:
bioconductor-annotationdbi
>=1.60.0,<1.61.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-gtools
>=3.5.0
r-mapplots
>=1.5
r-rcpp
>=0.11.5
r-vioplot
>=0.2
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-gofuncr
and update with:
conda update bioconductor-gofuncr
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-gofuncr:<tag>
(see bioconductor-gofuncr/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-gofuncr/README.html)