Statistical analysis and visualization of functional profiles for genes and gene clusters (original) (raw)

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

• barplot

• cnetplot

• dotplot

• emapplot

• gseaplot

• goplot

• upsetplot