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

Homepage: https://guangchuangyu.github.io/software/clusterProfiler/

Documentation: https://guangchuangyu.github.io/software/clusterProfiler/documentation/

Issue/Question: https://guangchuangyu.github.io/software/clusterProfiler/#feedback

Citation

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. doi:10.1089/omi.2011.0118

Overview

Supported ontologies/pathways

• 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 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
• 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)