recipe bioconductor-gofuncr

Gene ontology enrichment using FUNC

Homepage

https://bioconductor.org/packages/3.10/bioc/html/GOfuncR.html

License

GPL (>= 2)

Recipe

/bioconductor-gofuncr/meta.yaml

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 (07-Oct-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.

package bioconductor-gofuncr

Versions

1.6.0-0, 1.4.0-1, 1.2.0-0

Depends

• bioconductor-annotationdbi >=1.48.0,<1.49.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-iranges >=2.20.0,<2.21.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-gtools >=3.5.0

• r-mapplots >=1.5

• r-rcpp >=0.11.5

• r-vioplot >=0.2

Required By

• bioconductor-abaenrichment

Installation

With an activated Bioconda channel (see 2. 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>)

Link to this page

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