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


  • barplot
  • cnetplot
  • dotplot
  • emapplot
  • gseaplot
  • goplot
  • upsetplot


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


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.