{"id":13719417,"url":"https://github.com/YuLab-SMU/clusterProfiler","last_synced_at":"2025-05-07T11:31:39.748Z","repository":{"id":17557101,"uuid":"20360040","full_name":"YuLab-SMU/clusterProfiler","owner":"YuLab-SMU","description":":bar_chart: A universal enrichment tool for interpreting omics data","archived":false,"fork":false,"pushed_at":"2025-04-14T05:14:22.000Z","size":15857,"stargazers_count":1080,"open_issues_count":341,"forks_count":259,"subscribers_count":44,"default_branch":"devel","last_synced_at":"2025-04-14T06:25:33.932Z","etag":null,"topics":["enrichment-analysis","go","gsea","kegg","rstats","visualization"],"latest_commit_sha":null,"homepage":"https://yulab-smu.top/biomedical-knowledge-mining-book/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/YuLab-SMU.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS","contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2014-05-31T16:34:32.000Z","updated_at":"2025-04-14T05:14:26.000Z","dependencies_parsed_at":"2024-04-11T02:28:48.833Z","dependency_job_id":"8ac210ba-1138-4ee9-aca2-3affbb7dcfa4","html_url":"https://github.com/YuLab-SMU/clusterProfiler","commit_stats":{"total_commits":1113,"total_committers":40,"mean_commits":27.825,"dds":0.4582210242587601,"last_synced_commit":"12eaf2dfb14da5c10911cc7655890be271cb2269"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2FclusterProfiler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2FclusterProfiler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2FclusterProfiler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2FclusterProfiler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/YuLab-SMU","download_url":"https://codeload.github.com/YuLab-SMU/clusterProfiler/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252868890,"owners_count":21816933,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["enrichment-analysis","go","gsea","kegg","rstats","visualization"],"created_at":"2024-08-03T01:00:48.333Z","updated_at":"2025-05-07T11:31:37.180Z","avatar_url":"https://github.com/YuLab-SMU.png","language":"R","funding_links":[],"categories":["Table of Contents","R"],"sub_categories":["Bioinformatics"],"readme":"\n```{r echo=FALSE, results=\"hide\", message=FALSE}\nlibrary(\"badger\")\n#library(\"ypages\")\nBiocpkg \u003c- function (pkg) {\n    sprintf(\"[%s](http://bioconductor.org/packages/%s)\", pkg, pkg)\n}\n```\n\n\n#  clusterProfiler\n\n\u003cimg src=\"https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/clusterProfiler/clusterProfiler.png\" height=\"200\" align=\"right\" /\u003e\n\n[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n`r badge_bioc_release(\"clusterProfiler\", \"green\")`\n`r badge_devel(\"guangchuangyu/clusterProfiler\", \"green\")`\n[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since)\n\n\n\n[![platform](http://www.bioconductor.org/shields/availability/devel/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#archives)\n[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/clusterProfiler.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/clusterProfiler/)\n[![codecov](https://codecov.io/gh/GuangchuangYu/clusterProfiler/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/clusterProfiler/)\n\n\u003c!--\n[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/clusterProfiler/commits/master)\n--\u003e\n\n\n\n+ `r Biocpkg(\"clusterProfiler\")` supports exploring functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation.\n+ It provides a universal interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. \n+ It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation\n+ 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\n\n\nFor details, please visit:\n\n+ \u003chttps://yulab-smu.top/contribution-knowledge-mining/\u003e\n+ \u003chttps://yulab-smu.top/biomedical-knowledge-mining-book/\u003e\n\n\n\u003cimg src=\"graphic-abstract-The-Innovation-2021.jpg\" width=\"890\"/\u003e\n\n\n## :writing_hand: Authors\n\nGuangchuang YU  \u003chttps://yulab-smu.top\u003e\n\nSchool of Basic Medical Sciences, Southern Medical University\n\n\n------------------------------------------------------------------------\n\n\nIf you use `r Biocpkg(\"clusterProfiler\")` in published research, please cite the most appropriate paper(s) from this list:\n\n1. S Xu\u003csup\u003e#\u003c/sup\u003e, E Hu\u003csup\u003e#\u003c/sup\u003e, Y Cai\u003csup\u003e#\u003c/sup\u003e, Z Xie\u003csup\u003e#\u003c/sup\u003e, X Luo\u003csup\u003e#\u003c/sup\u003e, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, __G Yu__\u003csup\u003e\\*\u003c/sup\u003e. Using clusterProfiler to characterise Multi-Omics Data. __*Nature Protocols*__. 2024, accepted. \ndoi: [10.1038/s41596-024-01020-z](https://doi.org/10.1038/s41596-024-01020-z)\n2. T Wu\u003csup\u003e#\u003c/sup\u003e, E Hu\u003csup\u003e#\u003c/sup\u003e, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo\u003csup\u003e\\*\u003c/sup\u003e, **G Yu**\u003csup\u003e\\*\u003c/sup\u003e. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. **_The Innovation_**. 2021, 2(3):100141.\ndoi: [10.1016/j.xinn.2021.100141](https://doi.org/10.1016/j.xinn.2021.100141)\n3. __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.\ndoi: [10.1007/978-1-0716-0301-7_11](https://doi.org/10.1007/978-1-0716-0301-7_11)\n4. __G Yu__^\\*^. Using meshes for MeSH term enrichment and semantic analyses. __*Bioinformatics*__. 2018, 34(21):3766–3767.\ndoi: [10.1093/bioinformatics/bty410](https://doi.org/10.1093/bioinformatics/bty410)\n5. __G Yu__, QY He^\\*^. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. __*Molecular BioSystems*__. 2016, 12(2):477-479.\ndoi: [10.1039/C5MB00663E](https://doi.org/10.1039/C5MB00663E)\n6. __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.\ndoi: [10.1093/bioinformatics/btv145](https://doi.org/10.1093/bioinformatics/btv145)\n7. __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.\ndoi: [10.1093/bioinformatics/btu684](https://doi.org/10.1093/bioinformatics/btu684)\n8. __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.\ndoi: [10.1089/omi.2011.0118](https://doi.org/10.1089/omi.2011.0118)\n9. __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.\ndoi: [10.1093/bioinformatics/btq064](https://doi.org/10.1093/bioinformatics/btq064)\n\n\n\n\u003c!--\n\n\n\n r badge_custom(\"1st most cited paper\", \"in OMICS\", \"green\",\n  \"http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi\")`\n r badge_custom(\"ESI\", \"Highly Cited Paper\", \"green\")`\n r badge_doi(\"10.1089/omi.2011.0118\", \"green\")`\n\n\n------------------------------------------------------------------------\n\n### Citation\n\n\n\n\n\u003cimg src=\"https://guangchuangyu.github.io/software/citation_trend/clusterProfiler.png\" width=\"890\"/\u003e\n\n\n### Download stats\n\nr badge_download_bioc(\"clusterProfiler\")\nr badge_bioc_download(\"clusterProfiler\", \"total\", \"blue\")\nr badge_bioc_download(\"clusterProfiler\", \"month\", \"blue\")\n\n\n\u003cimg src=\"https://guangchuangyu.github.io/software/dlstats/clusterProfiler.png\" width=\"890\"/\u003e\n\n--\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FYuLab-SMU%2FclusterProfiler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FYuLab-SMU%2FclusterProfiler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FYuLab-SMU%2FclusterProfiler/lists"}