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 (from within R, enter 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 PDF R Script
Reference Manual PDF
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
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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 git@git.bioconductor.org: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