To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://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: 3.2
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:
## 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")
| CompGO-vignette.pdf | ||
| Introduction | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GO, GeneSetEnrichment, MultipleComparison, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (2 years) |
| License | GPL-2 |
| Depends | RDAVIDWebService |
| Imports | rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CompGO_1.6.0.tar.gz |
| Windows Binary | CompGO_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CompGO_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | CompGO_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CompGO/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/CompGO/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
