GOfuncR

DOI: 10.18129/B9.bioc.GOfuncR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GOfuncR.

Gene ontology enrichment using FUNC

Bioconductor version: 3.17

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>

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")

 

HTML	R Script	Introduction to GOfuncR
PDF		Reference Manual
Text		NEWS

Details

biocViews	GO, GeneSetEnrichment, Software
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 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
LinkingTo	Rcpp
Suggests	Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	GOfuncR_1.20.0.tar.gz
Windows Binary	GOfuncR_1.20.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	GOfuncR_1.19.0.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