Package: clusterProfiler 4.21.0

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. 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], Xiao Luo [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb]

clusterProfiler_4.21.0.tar.gz
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clusterProfiler_4.21.0.tgz(r-4.6-any)clusterProfiler_4.21.0.tgz(r-4.5-any)
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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-4.21.0(bioc 3.24)clusterProfiler-4.20.0(bioc 3.23)

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

15.89 score 1.2k stars 48 packages 23k scripts 2.2k mentions 73 exports 120 dependencies

Last updated from:400f57a5dc. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	225
linux-devel-x86_64	OK	384
source / vignettes	OK	271
linux-release-x86_64	OK	398
macos-release-arm64	OK	255
macos-oldrel-arm64	OK	232
windows-devel	OK	331
windows-release	OK	339
windows-oldrel	OK	407
wasm-release	OK	213

Exports:%<>%%>%append_kegg_category arrange bitr bitr_kegg browseKEGG buildGOmap cnetplot compareCluster dotplot download_KEGG dropGO emapplot enrichDAVID enricher enrichGO enrichKEGG enrichMKEGG enrichPC enrichWP filter geneID geneInCategory get_organism 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_WP heatplot idType interpret interpret_agent interpret_hierarchical ko2name merge_result mutate n plotGOgraph read.blast2go read.gaf read.gmt read.gmt.pc read.gmt.wp rename ridgeplot search_kegg_organism select setReadable simplify slice summarise uniprot_get

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem callr cli cluster cpp11 crayon curl DBI digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics 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 memoise mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo stringi stringr 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: 2025-11-20
Started: 2025-11-20

Help page	Topics
append_kegg_category	append_kegg_category
bitr	bitr
bitr_kegg	bitr_kegg
browseKEGG	browseKEGG
Compare gene clusters functional profile	compareCluster
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
get_wp_organism	get_wp_organisms
getPPI	getPPI
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_WP	gson_WP
idType	idType
Interpret Enrichment Results Using LLMs	interpret
Interpret enrichment results using a multi-agent pipeline (Deep Mode)	interpret_agent
Interpret enrichment results using a hierarchical strategy	interpret_hierarchical
ko2name	ko2name
merge_result	merge_result
plot	plot.interpretation
plotGOgraph	plotGOgraph
read.gmt.pc	read.gmt.pc
search_kegg_organism	search_kegg_organism
simplify method	simplify simplify,compareClusterResult-method simplify,enrichResult-method simplify,gseaResult-method
uniprot_get	uniprot_get

Package: clusterProfiler 4.21.0

clusterProfiler: A Universal Enrichment Tool for Interpreting Omics Data

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