GOfuncR

DOI: 10.18129/B9.bioc.GOfuncR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GOfuncR.

Gene ontology enrichment using FUNC

Bioconductor version: 3.8

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 (11-Oct-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. It is also possible to provide custom gene coordinates, annotations and ontologies.

Author: Steffi Grote

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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	1.2.0
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
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, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	ABAEnrichment
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GOfuncR_1.2.0.tar.gz
Windows Binary	GOfuncR_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	GOfuncR_1.2.0.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/
Package Downloads Report	Download Stats