bioconda / packages / bioconductor-gofuncr 1.8.0

Gene ontology enrichment using FUNC

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.8.0
  • osx-64  v1.8.0
To install this package with conda run one of the following:
conda install -c bioconda bioconductor-gofuncr
conda install -c bioconda/label/gcc7 bioconductor-gofuncr

Description

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 (23-Mar-2020). 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.

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