clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters
The clusterProfiler package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.
clusterProfiler is released within the Bioconductor project and the source code is hosted on GitHub.
Citation
Please cite the following article when using clusterProfiler:
Yu G, Wang L, Han Y and He Q*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Installation
Install clusterProfiler is easy, follow the guide on the Bioconductor page:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("clusterProfiler")
Overview
Supported Analyses
- 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)
- MeSH enrichment analysis (via meshes)
- 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
- enrichMap
- gseaplot
- plotGOgraph (via topGO package)
- upsetplot
Useful utilities:
- bitr (Biological Id TranslatoR)
- compareCluster (biological theme comparison)
- dropGO (screen out GO term of specific level or specific term)
- go2ont (convert GO ID to Ontology)
- go2term (convert GO ID to descriptive term)
- gofilter (restrict result at specific GO level)
- gsfilter (restrict result by gene set size)
- simplify (remove redundant GO terms, supported via GOSemSim)
Find out details and examples on Documentation.
Projects that depend on clusterProfiler
Other applications
- APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data
Feedback
- Please make sure you have followed the important guide before posting any issue/question
- For bugs or feature requests, please post to github issue
- For user questions, please post to Bioconductor support site and Biostars. We are following every post tagged with clusterProfiler
- Join the group chat on and