Overview
clusterProfiler implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.
Supported Analysis
- Over-Representation Analysis
- Gene Set Enrichment Analysis
- Biological theme comparison
Supported ontologies/pathways
- Disease Ontology (via DOSE)
- Network of Cancer Gene (via DOSE)
- DisGeNET (via DOSE)
- Gene Ontology (supports many species with GO annotation query online via AnnotationHub)
- KEGG Pathway and Module with latest online data (supports more than 4000 species listed in http://www.genome.jp/kegg/catalog/org_list.html)
- Reactome Pathway (via ReactomePA)
- DAVID (via RDAVIDWebService)
- Molecular Signatures Database
- hallmark gene sets
- positional gene sets
- curated gene sets
- motif gene sets
- computational gene sets
- GO gene sets
- oncogenic signatures
- immunologic signatures
- Other Annotations
- from other sources (e.g. DisGeNET as an example)
- user’s annotation
- customized ontology
- and many others
Visualization
- barplot
- cnetplot
- dotplot
- emapplot
- gseaplot
- goplot
- upsetplot
Vignette
Please go to https://yulab-smu.github.io/clusterProfiler-book/ for the full vignette.
Citation
If you use clusterProfiler in published research, please cite:
G Yu, LG Wang, Y Han, 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](http://dx.doi.org/10.1089/omi.2011.0118)
Need helps?
If you have questions/issues, please visit clusterProfiler homepage first. Your problems are mostly documented. If you think you found a bug, please follow the guide and provide a reproducible example to be posted on github issue tracker. For questions, please post to Bioconductor support site and tag your post with clusterProfiler.