CompGO
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CompGO.
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
Bioconductor version: 3.9
This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots.
Author: Sam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]
Maintainer: Ashley J. Waardenberg <A.Waardenberg at victorchang.edu.au>
citation("CompGO")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CompGO")
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("CompGO")| Introduction | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GO, GeneSetEnrichment, MultipleComparison, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL-2 |
| Depends | RDAVIDWebService |
| Imports | rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview |
| System Requirements | |
| URL |
See More
| Suggests | |
| 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 | CompGO_1.20.0.tar.gz |
| Windows Binary | CompGO_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | CompGO_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CompGO |
| Source Repository (Developer Access) | git clone [email protected]:packages/CompGO |
| Bioc Package Browser | https://code.bioconductor.org/browse/CompGO/ |
| Package Short Url | https://bioconductor.org/packages/CompGO/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |