Package: clusterProfiler
Type: Package
Title: A Universal Enrichment Tool for Interpreting Omics Data
Version: 4.21.3
Authors@R: c(
    person(given = "Guangchuang", family = "Yu",        email = "guangchuangyu@gmail.com",   role  = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
    person(given = "Li-Gen",      family = "Wang",      email = "reeganwang020@gmail.com",   role  = "ctb"),
    person(given = "Xiao",        family = "Luo",       email = "l77880853349@163.com",      role  = "ctb"),
    person(given = "Meijun",      family = "Chen",      email = "mjchen1996@outlook.com",    role  = "ctb"),
    person(given = "Giovanni",    family = "Dall'Olio", email = "giovanni.dallolio@upf.edu", role = "ctb"),
    person(given = "Wanqian",     family = "Wei",       email = "altair_wei@outlook.com",    role = "ctb"),
    person(given = "Chun-Hui",    family = "Gao",       email = "gaospecial@gmail.com",      role = "ctb", comment = c(ORCID = "0000-0002-1445-7939"))
	)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: 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.
Depends: R (>= 4.2.0)
Imports: aisdk, AnnotationDbi, dplyr, enrichit (>= 0.1.6), enrichplot
        (>= 1.9.3), ggplot2, GO.db, GOSemSim (>= 2.27.2), gson (>=
        0.0.7), httr, igraph, jsonlite, magrittr, methods, plyr,
        qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.2.3)
Suggests: AnnotationHub, BiocManager, DOSE, ggtangle, readr,
        org.Hs.eg.db, quarto, testthat
VignetteBuilder: quarto
ByteCompile: true
License: Artistic-2.0
URL: https://yulab-smu.top/contribution-knowledge-mining/
BugReports: https://github.com/YuLab-SMU/clusterProfiler/issues
Packaged: 2026-10-18 14:49:50 UTC; root
biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG,
        MultipleComparison, Pathways, Reactome, Visualization
Encoding: UTF-8
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-18 08:32:23 UTC
RemoteUrl: https://github.com/bioc/clusterProfiler
RemoteRef: HEAD
RemoteSha: bec51e53d2fddc753d9c6a755549bc486dc0232f
NeedsCompilation: no
Author: Guangchuang Yu [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>),
  Li-Gen Wang [ctb],
  Xiao Luo [ctb],
  Meijun Chen [ctb],
  Giovanni Dall'Olio [ctb],
  Wanqian Wei [ctb],
  Chun-Hui Gao [ctb] (ORCID: <https://orcid.org/0000-0002-1445-7939>)