clusterProfiler

This package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.

It supports both hypergeometric test and Gene Set Enrichment Analysis for many ontologies/pathways, including:

• Disease Ontology (via DOSE)
• Network of Cancer Gene (via DOSE)
• Gene Ontology (supports many species with GO annotation query online via AnnotationHub)
• KEGG Pathway and Module with latest online data (supports more than 2000 species listed in http://www.genome.jp/kegg/catalog/org_list.html)
• Reactome Pathway (via ReactomePA)
• DAVID (via RDAVIDWebService)
• Molecular Signatures Database
  • hallmark gene sets
  • positional gene sets
  • curated gene sets
  • motif gene sets
  • computational gene sets
  • GO gene sets
  • oncogenic signatures
  • immunologic signatures
• Other Annotations
  • from other sources (e.g. DisGeNET as an example)
  • user's annotation
  • customized ontology
  • and many others

clusterProfiler also provides several visualization methods to help interpreting enriched results, including:

• barplot
• cnetplot
• dotplot
• enrichMap
• gseaplot
• plotGOgraph (via topGO package)
• upsetplot

and several useful utilities:

• bitr (Biological Id TranslatoR)
• bitr_kegg (bitr using KEGG source)
• compareCluster (biological theme comparison)
• dropGO (screen out GO term of specific level or specific term)
• go2ont (convert GO ID to Ontology)
• go2term (convert GO ID to descriptive term)
• gofilter (restrict result at specific GO level)
• gsfilter (restrict result by gene set size)
• search_kegg_organism (search kegg supported organism)
• setReadable (convert IDs stored enrichResult object to gene symbol)
• simplify (remove redundant GO terms, supported via GOSemSim)

A discussion forum can be found at https://groups.google.com/forum/#!forum/clusterprofiler.

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://guangchuangyu.github.io

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:

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

Documentation

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

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

More documents can be found in http://www.bioconductor.org/packages/DOSE, http://www.bioconductor.org/packages/clusterProfiler and http://guangchuangyu.github.io/tags/clusterprofiler.

Bugs/Feature requests

• If you have any, let me know. Thx!