To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CompGO")

In most cases, you don't need to download the package archive at all.

CompGO

An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Bioconductor version: Release (3.0)

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 and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CompGO")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CompGO")

 

PDF CompGO-vignette.pdf
PDF R Script Introduction
PDF   Reference Manual
Text   NEWS

Details

biocViews GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 1.2.0
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-2
Depends RDAVIDWebService
Imports rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source CompGO_1.2.0.tar.gz
Windows Binary CompGO_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CompGO_1.2.0.tgz
Mac OS X 10.9 (Mavericks) CompGO_1.2.0.tgz
Browse/checkout source (username/password: readonly)
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