GOfuncR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GOfuncR.
Gene ontology enrichment using FUNC
Bioconductor version: 3.9
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 (27-Mar-2019). 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>
citation("GOfuncR")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | GO, GeneSetEnrichment, Software |
| Version | 1.4.0 |
| 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, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | ABAEnrichment |
| 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_1.4.0.tar.gz |
| Windows Binary | GOfuncR_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | GOfuncR_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOfuncR |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |