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# clusterProfiler <img src="" height="200" align="right" /> [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](]( [![](]( [![](]( [![Bioc](]( [![platform](]( [![Build Status](]( [![Linux/Mac Travis Build Status](]( [![AppVeyor Build Status](]( [![codecov](]( <!-- [![Last-changedate](]( --> - [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 <>. <img src="graphic-abstract-The-Innovation-2021.jpg" width="890"/> ## :writing_hand: Authors Guangchuang YU <> School of Basic Medical Sciences, Southern Medical University [![Twitter](]( [![saythanks](]( [![](]( ------------------------------------------------------------------------ If you use [clusterProfiler]( in published research, please cite the most appropriate paper(s) from this list: 1. T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>\*</sup>, **G Yu**<sup>\*</sup>. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. ***The Innovation***. 2021, 2(3):100141. doi: [10.1016/j.xinn.2021.100141]( 2. **G Yu**<sup>\*</sup>. 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]( 3. **G Yu**<sup>\*</sup>. Using meshes for MeSH term enrichment and semantic analyses. ***Bioinformatics***. 2018, 34(21):3766–3767. doi: [10.1093/bioinformatics/bty410]( 4. **G Yu**, QY He<sup>\*</sup>. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. ***Molecular BioSystems***. 2016, 12(2):477-479. doi: [10.1039/C5MB00663E]( 5. **G Yu**<sup>\*</sup>, LG Wang, and QY He<sup>\*</sup>. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. ***Bioinformatics***. 2015, 31(14):2382-2383. doi: [10.1093/bioinformatics/btv145]( 6. **G Yu**<sup>\*</sup>, LG Wang, GR Yan, QY He<sup>\*</sup>. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. ***Bioinformatics***. 2015, 31(4):608-609. doi: [10.1093/bioinformatics/btu684]( 7. **G Yu**, LG Wang, Y Han and QY He<sup>\*</sup>. 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]( 8. **G Yu**, F Li, Y Qin, X Bo<sup>\*</sup>, Y Wu, S Wang<sup>\*</sup>. 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]( <!-- r badge_custom("1st most cited paper", "in OMICS", "green", "")` r badge_custom("ESI", "Highly Cited Paper", "green")` r badge_doi("10.1089/omi.2011.0118", "green")` ------------------------------------------------------------------------ ### Citation <img src="" width="890"/> ### Download stats r badge_download_bioc("clusterProfiler") r badge_bioc_download("clusterProfiler", "total", "blue") r badge_bioc_download("clusterProfiler", "month", "blue") <img src="" width="890"/> -->