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

Bioconductor version: 2.14

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 Bassett [aut], Ash Waardenberg [aut, cre]

Maintainer: Ash Waardenberg <A.Waardenberg at>

Citation (from within R, enter citation("CompGO")):


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PDF R Script Introduction
PDF   Reference Manual
Text   NEWS


biocViews GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-2
Depends RDAVIDWebService
Imports rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene
System Requirements
Depends On Me
Imports Me
Suggests Me

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