README.md

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

clusterProfiler

• 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/

:writing_hand: Authors

Guangchuang YU https://yulab-smu.top

School of Basic Medical Sciences, Southern Medical University

If you use 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
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
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
4. G Yu*. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766–3767. doi: 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
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
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
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
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

YuLab-SMU/clusterProfiler documentation built on Nov. 14, 2024, 3:10 a.m.