CompGO

DOI: 10.18129/B9.bioc.CompGO    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 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: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version	1.28.0
In Bioconductor since	BioC 2.14 (R-3.1) (7.5 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_1.28.0.tar.gz
Windows Binary	CompGO_1.28.0.zip
macOS 10.13 (High Sierra)	CompGO_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CompGO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CompGO
Package Short Url	https://bioconductor.org/packages/CompGO/
Package Downloads Report	Download Stats