# clusterProfiler <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/clusterProfiler/clusterProfiler.png" height="200" align="right" /> [](http://www.repostatus.org/#active) [](https://www.bioconductor.org/packages/clusterProfiler) [](https://github.com/guangchuangyu/clusterProfiler) [](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since) [](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/clusterProfiler/) [](https://codecov.io/gh/GuangchuangYu/clusterProfiler/) <!-- [](https://github.com/GuangchuangYu/clusterProfiler/commits/master) --> - [clusterProfiler](http://bioconductor.org/packages/clusterProfiler) supports exploring functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. - It provides a universal 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 For details, please visit: - <https://yulab-smu.top/contribution-knowledge-mining/> - <https://yulab-smu.top/biomedical-knowledge-mining-book/> <img src="graphic-abstract-The-Innovation-2021.jpg" width="890"/> ## :writing_hand: Authors Guangchuang YU <https://yulab-smu.top> School of Basic Medical Sciences, Southern Medical University ------------------------------------------------------------------------ If you use [clusterProfiler](http://bioconductor.org/packages/clusterProfiler) in published research, please cite the most appropriate paper(s) from this list: 1. S Xu^\#, E Hu^\#, Y Cai^\#, Z Xie^\#, X Luo^\#, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, **G Yu**^\*. Using clusterProfiler to characterise Multi-Omics Data. ***Nature Protocols***. 2024, accepted. doi: [10.1038/s41596-024-01020-z](https://doi.org/10.1038/s41596-024-01020-z) 2. T Wu^\#, E Hu^\#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo^\*, **G Yu**^\*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. ***The Innovation***. 2021, 2(3):100141. doi: [10.1016/j.xinn.2021.100141](https://doi.org/10.1016/j.xinn.2021.100141) 3. **G Yu**^\*. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. ***Methods in Molecular Biology***. 2020, 2117:207-215. Humana, New York, NY. doi: [10.1007/978-1-0716-0301-7_11](https://doi.org/10.1007/978-1-0716-0301-7_11) 4. **G Yu**^\*. Using meshes for MeSH term enrichment and semantic analyses. ***Bioinformatics***. 2018, 34(21):3766–3767. doi: [10.1093/bioinformatics/bty410](https://doi.org/10.1093/bioinformatics/bty410) 5. **G Yu**, QY He^\*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. ***Molecular BioSystems***. 2016, 12(2):477-479. doi: [10.1039/C5MB00663E](https://doi.org/10.1039/C5MB00663E) 6. **G Yu**^\*, LG Wang, and QY He^\*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. ***Bioinformatics***. 2015, 31(14):2382-2383. doi: [10.1093/bioinformatics/btv145](https://doi.org/10.1093/bioinformatics/btv145) 7. **G Yu**^\*, LG Wang, GR Yan, QY He^\*. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. ***Bioinformatics***. 2015, 31(4):608-609. doi: [10.1093/bioinformatics/btu684](https://doi.org/10.1093/bioinformatics/btu684) 8. **G Yu**, LG Wang, Y Han and QY He^\*. clusterProfiler: an R package for comparing biological themes among gene clusters. ***OMICS: A Journal of Integrative Biology***. 2012, 16(5):284-287. doi: [10.1089/omi.2011.0118](https://doi.org/10.1089/omi.2011.0118) 9. **G Yu**, F Li, Y Qin, X Bo^\*, Y Wu, S Wang^\*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. ***Bioinformatics***. 2010, 26(7):976-978. doi: [10.1093/bioinformatics/btq064](https://doi.org/10.1093/bioinformatics/btq064) <!-- &#10; &#10; r badge_custom("1st most cited paper", "in OMICS", "green", "http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi")` r badge_custom("ESI", "Highly Cited Paper", "green")` r badge_doi("10.1089/omi.2011.0118", "green")` &#10; ------------------------------------------------------------------------ &#10;### Citation &#10; &#10; <img src="https://guangchuangyu.github.io/software/citation_trend/clusterProfiler.png" width="890"/> &#10; ### Download stats &#10;r badge_download_bioc("clusterProfiler") r badge_bioc_download("clusterProfiler", "total", "blue") r badge_bioc_download("clusterProfiler", "month", "blue") &#10; <img src="https://guangchuangyu.github.io/software/dlstats/clusterProfiler.png" width="890"/> &#10;-->