GOfuncR

DOI: 10.18129/B9.bioc.GOfuncR    

Gene ontology enrichment using FUNC

Bioconductor version: Release (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. From version 0.99.14 on it is also possible to provide custom annotations and ontologies.

Author: Steffi Grote

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

Citation (from within R, enter citation("GOfuncR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GOfuncR")

Documentation

HTML R Script Introduction to GOfuncR
PDF   Reference Manual
Text   NEWS

Details

biocViews GO, GeneSetEnrichment, Software
Version 1.0.0
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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GOfuncR_1.0.0.tar.gz
Windows Binary GOfuncR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GOfuncR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOfuncR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOfuncR
Package Short Url http://bioconductor.org/packages/GOfuncR/
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