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8.4 years ago
Guangchuang Yu
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The clusterProfiler package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.
Homepage: https://guangchuangyu.github.io/software/clusterProfiler/
Documentation: https://guangchuangyu.github.io/software/clusterProfiler/documentation/
Issue/Question: https://guangchuangyu.github.io/software/clusterProfiler/#feedback
Citation
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. doi:10.1089/omi.2011.0118
Overview
Supported ontologies/pathways
- Disease Ontology (via DOSE)
- Network of Cancer Gene (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
- 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)
