Welcome to the new bioconductor.org!

GOfuncR

Gene ontology enrichment using FUNC


Bioconductor version: Release (3.18)

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.

Author: Steffi Grote

Maintainer: Steffi Grote <grote.steffi at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GOfuncR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GOfuncR")
Introduction to GOfuncR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GO, GeneSetEnrichment, Software
Version 1.22.2
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
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), IRanges, AnnotationDbi, utils, grDevices, graphics, stats
System Requirements
URL
See More
Suggests Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GOfuncR_1.22.2.tar.gz
Windows Binary GOfuncR_1.22.2.zip
macOS Binary (x86_64) GOfuncR_1.22.2.tgz
macOS Binary (arm64) GOfuncR_1.22.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOfuncR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOfuncR
Bioc Package Browser https://code.bioconductor.org/browse/GOfuncR/
Package Short Url https://bioconductor.org/packages/GOfuncR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive