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This is the development version of clusterProfiler; for the stable release version, see clusterProfiler.

A universal enrichment tool for interpreting omics data

Bioconductor version: Development (3.19)

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Author: Guangchuang Yu [aut, cre, cph] , Li-Gen Wang [ctb], Erqiang Hu [ctb], Xiao Luo [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("clusterProfiler")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Statistical analysis and visualization of functional profiles for genes and gene clusters HTML R Script
Reference Manual PDF


biocViews Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization
Version 4.11.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, downloader, DOSE(>= 3.23.2), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim(>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.0.7)
System Requirements
URL https://yulab-smu.top/biomedical-knowledge-mining-book/(docs) https://doi.org/10.1016/j.xinn.2021.100141(paper)
Bug Reports https://github.com/GuangchuangYu/clusterProfiler/issues
See More
Suggests AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat
Linking To
Depends On Me maEndToEnd
Imports Me bioCancer, CBNplot, CEMiTool, CeTF, debrowser, EasyCellType, eegc, enrichTF, esATAC, ExpHunterSuite, famat, GDCRNATools, goSorensen, IRISFGM, MAGeCKFlute, MetaPhOR, methylGSA, MicrobiomeProfiler, miRSM, miRspongeR, Moonlight2R, MoonlightR, PanomiR, pathlinkR, Pigengene, recountWorkflow, seqArchRplus, signatureSearch, TCGAWorkflow, TimiRGeN
Suggests Me ChIPseeker, cola, DAPAR, DOSE, enrichplot, EpiCompare, EpiMix, GeneTonic, GenomicSuperSignature, GeoTcgaData, ggkegg, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, org.Mxanthus.db, paxtoolsr, ReactomePA, rrvgo, scFeatures, scGPS, simplifyEnrichment, TCGAbiolinks, tidybulk, vsclust
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package clusterProfiler_4.11.0.tar.gz
Windows Binary clusterProfiler_4.11.0.zip
macOS Binary (x86_64) clusterProfiler_4.11.0.tgz
macOS Binary (arm64) clusterProfiler_4.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/clusterProfiler
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clusterProfiler
Bioc Package Browser https://code.bioconductor.org/browse/clusterProfiler/
Package Short Url https://bioconductor.org/packages/clusterProfiler/
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