GOaGO
This is the released version of GOaGO; for the devel version, see GOaGO.
Gene Ontology enrichment analysis of gene pairs
Bioconductor version: Release (3.23)
GO-a-GO annotates Gene Ontology terms that are enriched in a given set of gene pairs. The enrichment is calculated from a permutation test for overrepresentation of gene pairs that are associated with a shared term. Such gene pairs are counted for the original set of gene pairs and compared against randomized sets in which the structure of the pairs is preserved, but the gene identities (including the associated terms) are permuted.
Author: Aleksander Jankowski [aut, cre]
Maintainer: Aleksander Jankowski <aleksander.jankowski at uw.edu.pl>
citation("GOaGO")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOaGO")
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("GOaGO")| Gene Ontology enrichment analysis of gene pairs with GO-a-GO | HTML | R Script |
| Reference Manual |
Details
| biocViews | GO, GeneSetEnrichment, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), methods |
| Imports | AnnotationDbi, BiocGenerics, BiocParallel, clusterProfiler, data.table, DOSE, GenomeInfoDb, GenomicRanges, ggplot2, ggridges, Matrix, qvalue, S4Vectors |
| System Requirements | |
| URL | https://github.com/ajank/GOaGO |
| Bug Reports | https://github.com/ajank/GOaGO/issues |
See More
| Suggests | BiocStyle, GenomicInteractions, ggrepel, knitr, org.Hs.eg.db, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Linking To | |
| 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 | GOaGO_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | GOaGO_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOaGO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GOaGO |
| Bioc Package Browser | https://code.bioconductor.org/browse/GOaGO/ |
| Package Short Url | https://bioconductor.org/packages/GOaGO/ |
| Package Downloads Report | Download Stats |