DOI: 10.18129/B9.bioc.GOfuncR    

This is the development version of GOfuncR; to use it, please install the devel version of Bioconductor.

Gene ontology enrichment using FUNC

Bioconductor version: Development (3.7)

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 (10-Apr-2018). 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.

Author: Steffi Grote

Maintainer: Steffi Grote <steffi_grote at eva.mpg.de>

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biocViews GO, GeneSetEnrichment, Software
Version 0.99.13
License GPL (>= 2)
Depends R (>= 3.4), vioplot (>= 0.2)
Imports Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges(>= 1.28.4), AnnotationDbi, utils, grDevices, graphics, stats
LinkingTo Rcpp
Suggests Homo.sapiens, BiocStyle, knitr, testthat
Depends On Me
Imports Me
Suggests Me
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Source Repository git clone https://git.bioconductor.org/packages/GOfuncR
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