clusterProfiler specifications


Unique identifier OMICS_13440
Name clusterProfiler
Alternative name cluster Profiler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 3.8.1
Stability Stable
qvalue, AnnotationDbi, methods, stats, KEGG.db, plyr, utils, testthat, ggplot2, knitr, GO.db,, AnnotationHub, GOSemSim, GSEABase, tidyr, magrittr, R(>=3.4.0), ReactomePA, prettydoc, pathview, DOSE(>=3.5.1), enrichplot(>=0.99.7), rvcheck
Maintained Yes


  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • enrichGO
  • enrichKEGG
  • groupGO



Add your version



  • person_outline Guangchuang Yu <>

Publications for clusterProfiler

clusterProfiler institution(s)
State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
clusterProfiler funding source(s)
This work was supported by National ‘‘973’’ Projects of China (2011CB910700), the 2007 Chang-Jiang Scholars Program, ‘‘211’’ Projects, National Natural Science Foundation of China (20871057), Guangdong Natural Science Research Grant (32209003), and the Fundamental Research Funds for the Central Universities (21611303 and 11610101).

clusterProfiler review

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One of the best packages out there to perform functional analyses (e.g. over-representation, GSEA, bio-theme). It has also pretty ggplot2-based plotting functions to visually communicate your results. In addition, it supports many ontologies/pathways db, such as: Gene Ontology (Amigo), KEGG, DAVID, Reactome, Disease Ontology, Molecular Signature Databases and CUSTOM DBs. In my point of view, plotting functionalities are fast and pretty, especially the clusterprofileR::barplot() and ::dotplot() functions. At last, documentation is example-driven and is more than enough to understand and use the package really quickly. As a final note, the author is very attentive to help beginners in forums and alikes, and the code runs smoothly and fast in non-workstation machines.