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:https://www.genome.jp/kegg/catalog/org_list.html)
• Reactome Pathway (via ReactomePA)
• 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
• DAVID (via RDAVIDWebService)
• 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:

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

and several useful utilities:

• gofilter (restrict the result at specific GO level)
• dropGO (screen out GO term of specific level or specific term)
• simplify (remove redundant GO terms, supported via GOSemSim)

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

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

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:https://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118

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

To install:

• the latest released version: biocLite("clusterProfiler")
• the latest development version: devtools::install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler"))

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:https://www.bioconductor.org/packages/DOSE, http:https://www.bioconductor.org/packages/ReactomePA and http:https://guangchuangyu.github.io/tags/clusterprofiler.

• If you have any, let me know. Thx!