Package: GOfuncR 1.25.0
Steffi Grote
GOfuncR: 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 (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.
Authors:
GOfuncR_1.25.0.tar.gz
GOfuncR_1.25.0.zip(r-4.5)GOfuncR_1.25.0.zip(r-4.4)GOfuncR_1.25.0.zip(r-4.3)
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GOfuncR.pdf |GOfuncR.html✨
GOfuncR/json (API)
NEWS
| # Install 'GOfuncR' in R: |
| install.packages('GOfuncR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GOfuncR-1.25.0(bioc 3.20)GOfuncR-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:89fed0888c
Exports:get_anno_categoriesget_anno_genesget_child_nodesget_idsget_namesget_parent_nodesgo_enrichplot_anno_scoresrefine
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegtoolshttrIRangesjsonliteKEGGRESTlatticelifecyclemapplotsmemoisemimeopensslpkgconfigplogrpngR6RcpprlangRSQLiteS4VectorssmsysUCSC.utilsvctrsvioplotXVectorzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get all associated ontology categories for the input genes | get_anno_categories |
| Get genes that are annotated to GO-categories | get_anno_genes |
| Get all child nodes of gene ontology categories | get_child_nodes |
| Get the ID of a GO-category given its name | get_ids |
| Get the full names of gene ontology categories given the IDs | get_names |
| Get all parent nodes of gene ontology categories | get_parent_nodes |
| Test gene sets for enrichment in GO-categories | go_enrich |
| Plot distribution of scores of genes annotated to GO-categories | plot_anno_scores |
| Refine results given a FWER threshold | refine |
