clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

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

clusterProfiler is released within the Bioconductor project and the source code is hosted on GitHub.


Guangchuang Yu, School of Basic Medical Sciences, Southern Medical University.


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.


Install clusterProfiler is easy, follow the guide on the Bioconductor page:

## try http:// if https:// URLs are not supported
## biocLite("BiocUpgrade") ## you may need this


Supported Analyses

  • Over-Representation Analysis
  • Gene Set Enrichment Analysis
  • Biological theme comparison

Supported ontologies/pathways


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

Useful utilities:

  • bitr (Biological Id TranslatoR)
  • 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)
  • simplify (remove redundant GO terms, supported via GOSemSim)

Find out details and examples on Documentation.

Projects that depend on clusterProfiler

Other applications

  • APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data