Overview

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

Supported Analysis

Over-Representation Analysis
Gene Set Enrichment Analysis
Biological theme comparison

Supported ontologies/pathways

Disease Ontology (via DOSE)
Network of Cancer Gene (via DOSE)
DisGeNET (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 4000 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

Visualization

barplot
cnetplot
dotplot
emapplot
gseaplot
goplot
upsetplot

Vignette

Please go to https://yulab-smu.github.io/clusterProfiler-book/ for the full vignette.

Citation

If you use clusterProfiler in published research, please cite:

G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)

Need helps?

If you have questions/issues, please visit clusterProfiler homepage first. Your problems are mostly documented. If you think you found a bug, please follow the guide and provide a reproducible example to be posted on github issue tracker. For questions, please post to Bioconductor support site and tag your post with clusterProfiler.