Package: clusterProfiler 4.21.5

Guangchuang Yu

clusterProfiler: A Universal Enrichment Tool for Interpreting Omics Data

A universal tool for interpreting functional characteristics of omics data. It supports Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) for both coding and non-coding genomics data of thousands of species. It provides a unified and tidy interface to access, manipulate, and visualize enrichment results. A key capability is the simultaneous analysis and comparison of datasets from multiple treatments or time points. It also provides high-level access to topology-aware enrichment workflows powered by 'enrichit', including single-network and multi-layer network enrichment for Gene Ontology and KEGG analyses. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.

Authors:Guangchuang Yu [aut, cre, cph], Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb], Qianwen Wang [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb]

clusterProfiler_4.21.5.tar.gz
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clusterProfiler_4.21.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clusterProfiler/json (API)

# Install 'clusterProfiler' in R:

install.packages('clusterProfiler', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/clusterprofiler/issues

Datasets:

DE_GSE8057 - Datasets gcSample contains a sample of gene clusters.
gcSample - Datasets gcSample contains a sample of gene clusters.

On BioConductor:clusterProfiler-4.21.4(bioc 3.24)clusterProfiler-4.20.3(bioc 3.23)

annotation clustering genesetenrichment go kegg multiplecomparison pathways reactome visualization enrichment-analysis gsea quarto

18.12 score 1.2k stars 63 packages 25k scripts 62k downloads 2.2k mentions 121 exports 129 dependencies

Last updated from:978eabaee5. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	269
linux-devel	ERROR	843
source / vignettes	OK	329
linux-release	ERROR	913
macos-release	ERROR	974
macos-oldrel	ERROR	1123
windows-devel	ERROR	817
windows-release	ERROR	813
windows-oldrel	ERROR	572
wasm-release	OK	180

Exports:%<>%%>%add_go_level adjudicate aggregate_enrichment aggregate_omics append_kegg_category arrange ask attribute_genes bayes_enrich bayes_summary bitr bitr_kegg browseKEGG buildGOmap chat cnetplot collapse_findings compareCluster consensus_findings dotplot download_KEGG dropGO emapplot enrichDAVID enricher enrichGO enrichKEGG enrichMKEGG enrichPC enrichWP evidence evidence_biotrigger evidence_perturbation evidence_ppi evidence_status filter fork_dialogue geneID geneInCategory get_organism get_ppi get_ppi_network get_wp_organisms getPPI getTaxID getTaxInfo Gff2GeneTable go2ont go2term gofilter goplot group_by groupGO GSEA gseaplot gseGO gseKEGG gseMKEGG gsePC gseWP gsfilter gson_GO gson_GO_local gson_KEGG gson_KEGG_mapper gson_KO gson_WP harmonize_ids heatplot idType interpret interpret_agent interpret_dialogue interpret_hierarchical ko2name mechanism_alias_regulator mechanism_discover mechanism_graph mechanism_preflight mechanism_report mechanism_reproduction mechanism_sets mechanism_significant mechanism_tfunion mechanism_writable mechanism_xref merge_result mnseGO mnseKEGG mnseMKEGG mnseWP mutate n nseGO nseKEGG nseMKEGG nseWP pathway_evidence plot_mechanism plot_mechanism_tree plotGOgraph provenance read.blast2go read.gaf read.gmt read.gmt.pc read.gmt.wp reduce_redundancy rename ridgeplot say search_kegg_organism select select_features_for_ora setReadable simplify slice summarise uniprot_get

Dependencies:abind aisdk AnnotationDbi ape aplot askpass base64enc Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob bslib cachem callr cli cluster cpp11 crayon curl DBI DelayedArray digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils

Statistical analysis and visualization of functional profiles for genes and gene clusters

Rendered fromclusterProfiler.qmdusingquarto::html

Last update: 2026-06-24
Started: 2025-11-20

Help page	Topics
Add the GO level of each enriched term	add_go_level
Decide which mechanisms the evidence actually supports	adjudicate
append_kegg_category	append_kegg_category
Send a question to an evidence dialogue	ask
Attribute each gene to the regulator that best explains it	attribute_genes
bitr	bitr
bitr_kegg	bitr_kegg
browseKEGG	browseKEGG
Chat about an evidence bundle, turn by turn	chat
Collapse redundant findings before reporting them	collapse_findings print.collapsedFindings
Compare gene clusters functional profile	compareCluster
The findings an adjudication allows you to talk about	consensus_findings
Datasets gcSample contains a sample of gene clusters.	DataSet DE_GSE8057 gcSample kegg_category kegg_species
download_KEGG	download_KEGG
dropGO	dropGO
enrichDAVID	enrichDAVID
enricher	enricher
GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.	enrichGO
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.	enrichKEGG
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.	enrichMKEGG
enrichPC	enrichPC
enrichWP	enrichWP
Grade upstream evidence for a gene list	evidence
Upstream regulators from GPSAdb's biotrigger	evidence_biotrigger
Perturbation evidence from GPSAdb	evidence_perturbation
Network evidence for a gene list	evidence_ppi
Evidence status of every gene named in an interpretation	evidence_status
Fork a dialogue to explore a side question	fork_dialogue
get_ppi_network	get_ppi_network
get_wp_organism	get_wp_organisms
getPPI	getPPI get_ppi
getTaxID	getTaxID
getTaxInfo	getTaxInfo
Gff2GeneTable	Gff2GeneTable
go2ont	go2ont
go2term	go2term
gofilter	gofilter
Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.	groupGO
Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.	groupGOResult-class show,groupGOResult-method
GSEA	GSEA
gseGO	gseGO
gseKEGG	gseKEGG
gseMKEGG	gseMKEGG
gsePC	gsePC
gseWP	gseWP
gson_KEGG	gson_GO
Build a gson object that annotate Gene Ontology	gson_GO_local
gson_KEGG	gson_KEGG
Build KEGG annotation for novel species using KEGG Mapper	gson_KEGG_mapper
gson_KO	gson_KO
gson_WP	gson_WP
idType	idType
Interpret Enrichment Results Using LLMs	interpret
Interpret enrichment results using a multi-agent pipeline (Deep Mode)	interpret_agent
Discuss an evidence bundle with a model	interpret_dialogue print.evidenceDialogue
Interpret enrichment results using a hierarchical strategy	interpret_hierarchical
Interpret an evidence bundle	interpret-evidence
ko2name	ko2name
Bring a regulator label to one spelling	mechanism_alias_regulator
Rank candidate transcription factors for a differential expression profile	mechanism_discover
The mechanism the evidence permits, as a mechgraph	mechanism_graph
Decide whether a dataset can support driver attribution at all	mechanism_preflight print.mechanismPreflight
Turn mechanism evidence into a verdict sheet and a next experiment	mechanism_report print.mechanismReport
Concordance of a pathway shift across independent perturbation datasets	mechanism_reproduction
Upstream gene-set collections for mechanism analysis	mechanism_sets
Which rows of a regulator table are significant	mechanism_significant
The transcription-factor union collection	mechanism_tfunion
The sentence an evidence level permits	mechanism_writable
Evidence level rules for upstream gene sets	mechanism_xref
merge_result	merge_result
mnseGO	mnseGO
mnseKEGG	mnseKEGG
mnseMKEGG	mnseMKEGG
mnseWP	mnseWP
nseGO	nseGO
nseKEGG	nseKEGG
nseMKEGG	nseMKEGG
nseWP	nseWP
Test enriched pathways against measured perturbation data	pathway_evidence print.pathway_evidence
Draw a mechanism graph	plot_mechanism
Draw the mechanism as a tree	plot_mechanism_tree
plot	plot.interpretation
plotGOgraph	plotGOgraph
Print an adjudication	print.adjudication
Print an evidence bundle	print.evidenceBundle
Execution provenance of an interpretation	provenance
read.gmt.pc	read.gmt.pc
Reduce redundant terms in an enrichment result before interpretation	reduce_redundancy
Tell an evidence dialogue something the data does not contain	say
search_kegg_organism	search_kegg_organism
simplify method	simplify simplify,compareClusterResult-method simplify,enrichResult-method simplify,gseaResult-method
uniprot_get	uniprot_get

Package: clusterProfiler 4.21.5

clusterProfiler: A Universal Enrichment Tool for Interpreting Omics Data

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