GOfuncR
This is the released version of GOfuncR; for the devel version, see GOfuncR.
Gene ontology enrichment using FUNC
Bioconductor version: Release (3.23)
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("GOfuncR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.31.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 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 |
| 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_1.31.0.tar.gz |
| Windows Binary (x86_64) | GOfuncR_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | GOfuncR_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | GOfuncR_1.31.0.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 |