sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

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. CompGO implements a log-odds ratio (z-score) statistic for determining statistical significance of GO term enrichment between experiments.

Getting started

Package details

Bioconductor views GO GeneSetEnrichment MultipleComparison Visualization
Maintainer
LicenseGPL-2
Version1.5.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("sam-bassett/CompGO")
sam-bassett/CompGO documentation built on May 25, 2017, 11:38 p.m.