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https://github.com/YuLab-SMU/clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://github.com/YuLab-SMU/clusterProfiler

enrichment-analysis go gsea kegg rstats visualization

Last synced: 3 months ago
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:bar_chart: A universal enrichment tool for interpreting omics data

Host: GitHub
URL: https://github.com/YuLab-SMU/clusterProfiler
Owner: YuLab-SMU
Created: 2014-05-31T16:34:32.000Z (over 10 years ago)
Default Branch: devel
Last Pushed: 2024-07-27T02:45:53.000Z (4 months ago)
Last Synced: 2024-07-27T05:36:55.416Z (4 months ago)
Topics: enrichment-analysis, go, gsea, kegg, rstats, visualization
Language: R
Homepage: https://yulab-smu.top/biomedical-knowledge-mining-book/
Size: 15.1 MB
Stars: 976
Watchers: 45
Forks: 250
Open Issues: 311
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS
- Contributing: CONTRIBUTING.md

Awesome Lists containing this project

jimsghstars - YuLab-SMU/clusterProfiler - :bar_chart: A universal enrichment tool for interpreting omics data (R)

README

        
```{r echo=FALSE, results="hide", message=FALSE}

library("badger")

#library("ypages")

Biocpkg <- function (pkg) {

    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)

}

```

#  clusterProfiler



[![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)

`r badge_bioc_release("clusterProfiler", "green")`

`r badge_devel("guangchuangyu/clusterProfiler", "green")`

[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since)

[![platform](http://www.bioconductor.org/shields/availability/devel/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#archives)

[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/clusterProfiler.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/clusterProfiler/)

[![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/clusterProfiler/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/clusterProfiler)

[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/clusterProfiler/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/clusterProfiler)

[![codecov](https://codecov.io/gh/GuangchuangYu/clusterProfiler/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/clusterProfiler/)

+ `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.

+ 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 .



## :writing_hand: Authors

Guangchuang YU  

School of Basic Medical Sciences, Southern Medical University

[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=clusterProfiler&url=http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118&screen_name=guangchuangyu)

[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)

`r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

------------------------------------------------------------------------

If you use `r Biocpkg("clusterProfiler")` in published research, please cite the most appropriate paper(s) from this list:

1. 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)

2. __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)

3. __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)

4. __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)

5. __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)

6. __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)

7. __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)

8. __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)