clusterProfiler

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://ygc.name

Citation

Please cite the following article when using clusterProfiler:

Yu G, Wang L, Han Y and He Q. 
clusterProfiler: an R package for comparing biological themes among gene clusters.
OMICS: A Journal of Integrative Biology, 2012, 16(5):284-287. 

URL: http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118

License

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

Installation

To install:

• the latest released version: biocLite("clusterProfiler")
• the latest development version:

install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler"))

Documentation

• Why clusterProfiler fails
• KEGG enrichment analysis with latest online data using clusterProfiler
• DAVID functional analysis with clusterProfiler
• use clusterProfiler as an universal enrichment analysis tool
• a formula interface for GeneOntology analysis <- bioinfoblog.it
• Enrichment map
• dotplot for enrichment result
• functional enrichment for GTEx paper
• functional enrichment analysis with NGS data

To view the vignette of clusterProfiler installed in your system, start R and enter:

vignette("clusterProfiler", package="clusterProfiler")

Bugs/Feature requests

• If you have any, let me know. Thx!