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

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