CompGO

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see CompGO.

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

Bioconductor version: 3.3

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), statistically compare gene ontology enrichment between multiple experiments and finally visualise and compare these enrichments using directed acyclic graphs or scatterplots. CompGO also enables clustering of experiments based on their GO profiles and provides functions for performing and visualising principle component analysis.

Author: Sam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]

Maintainer: Ashley J. Waardenberg <awaardenberg at cmri.org.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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")

Details

Package Archives

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