# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "clusterProfiler" in publications use:'
type: software
license: Artistic-2.0
title: 'clusterProfiler: A Universal Enrichment Tool for Interpreting Omics Data'
version: 4.20.0
doi: 10.1016/j.xinn.2024.100722
identifiers:
- type: doi
  value: 10.32614/CRAN.package.clusterProfiler
abstract: 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:
- family-names: Yu
  given-names: Guangchuang
  email: guangchuangyu@gmail.com
  orcid: https://orcid.org/0000-0002-6485-8781
preferred-citation:
  type: article
  title: Thirteen years of clusterProfiler
  authors:
  - family-names: Yu
    given-names: Guangchuang
    email: guangchuangyu@gmail.com
    orcid: https://orcid.org/0000-0002-6485-8781
  url: https://doi.org/10.1016/j.xinn.2024.100722
  doi: 10.1016/j.xinn.2024.100722
  journal: The Innovation
  month: '11'
  year: '2024'
  volume: '5'
  issue: '6'
  start: '100722'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/YuLab-SMU/clusterProfiler
commit: d67d9f6521e9cfaf4de0a64199407a609be01f49
url: https://yulab-smu.top/contribution-knowledge-mining/
date-released: '2026-04-28'
contact:
- family-names: Yu
  given-names: Guangchuang
  email: guangchuangyu@gmail.com
  orcid: https://orcid.org/0000-0002-6485-8781
references:
- type: article
  title: Using clusterProfiler to characterize multiomics data
  authors:
  - family-names: Xu
    given-names: Shuangbin
  - family-names: Hu
    given-names: Erqiang
  - family-names: Cai
    given-names: Yantong
  - family-names: Xie
    given-names: Zijing
  - family-names: Luo
    given-names: Xiao
  - family-names: Zhan
    given-names: Li
  - family-names: Tang
    given-names: Wenli
  - family-names: Wang
    given-names: Qianwen
  - family-names: Liu
    given-names: Bingdong
  - family-names: Wang
    given-names: Rui
  - family-names: Xie
    given-names: Wenqin
  - family-names: Wu
    given-names: Tianzhi
  - family-names: Xie
    given-names: Liwei
  - family-names: Yu
    given-names: Guangchuang
  url: https://www.nature.com/articles/s41596-024-01020-z
  doi: 10.1038/s41596-024-01020-z
  journal: Nature Protocols
  month: '11'
  year: '2024'
  volume: '19'
  issue: '11'
  start: 3292-3320
- type: article
  title: 'clusterProfiler 4.0: A universal enrichment tool for interpreting omics
    data'
  authors:
  - family-names: Wu
    given-names: Tianzhi
  - family-names: Hu
    given-names: Erqiang
  - family-names: Xu
    given-names: Shuangbin
  - family-names: Chen
    given-names: Meijun
  - family-names: Guo
    given-names: Pingfan
  - family-names: Dai
    given-names: Zehan
  - family-names: Feng
    given-names: Tingze
  - family-names: Zhou
    given-names: Lang
  - family-names: Tang
    given-names: Wenli
  - family-names: Zhan
    given-names: Li
  - family-names: Fu
    given-names: xiaochong
  - family-names: Liu
    given-names: Shanshan
  - family-names: Bo
    given-names: Xiaochen
  - family-names: Yu
    given-names: Guangchuang
  journal: The Innovation
  year: '2021'
  volume: '2'
  issue: '3'
  doi: 10.1016/j.xinn.2021.100141
  start: '100141'
- type: article
  title: 'clusterProfiler: an R package for comparing biological themes among gene
    clusters'
  authors:
  - family-names: Yu
    given-names: Guangchuang
  - family-names: Wang
    given-names: Li-Gen
  - family-names: Han
    given-names: Yanyan
  - family-names: He
    given-names: Qing-Yu
  journal: 'OMICS: A Journal of Integrative Biology'
  year: '2012'
  volume: '16'
  issue: '5'
  doi: 10.1089/omi.2011.0118
  start: 284-287