In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)

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

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.

YuLab-SMU/clusterProfiler documentation built on Nov. 14, 2024, 3:10 a.m.