clusterProfiler v3.0.4

by Guangchuang Yu

statistical analysis and visualization of functional profiles for genes and gene clusters

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Readme

clusterProfiler

platform Build Status Bioc post commit download gitter

This package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.

It supports both hypergeometric test and Gene Set Enrichment Analysis for many ontologies/pathways, including:

clusterProfiler also provides several visualization methods to help interpreting enriched results, including:

  • barplot
  • cnetplot
  • dotplot
  • enrichMap
  • gseaplot
  • plotGOgraph (via topGO package)
  • upsetplot

and several useful utilities:

  • bitr (Biological Id TranslatoR)
  • bitr_kegg (bitr using KEGG source)
  • 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)
  • search_kegg_organism (search kegg supported organism)
  • setReadable (convert IDs stored enrichResult object to gene symbol)
  • simplify (remove redundant GO terms, supported via GOSemSim)

A discussion forum can be found at https://groups.google.com/forum/#!forum/clusterprofiler.

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://guangchuangyu.github.io

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.

URL: http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118

License

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

Installation

To install:

  • the latest released version: biocLite("clusterProfiler")
  • the latest development version: devtools::install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler"))

Documentation

To view the vignette of clusterProfiler installed in your system, start R and enter:

vignette("clusterProfiler", package="clusterProfiler")

More documents can be found in http://www.bioconductor.org/packages/DOSE, http://www.bioconductor.org/packages/clusterProfiler and http://guangchuangyu.github.io/tags/clusterprofiler.

Bugs/Feature requests

Functions in clusterProfiler

Name Description
clusterProfiler-package statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
buildGOmap buildGOmap
enrichGO GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
gseMKEGG gseMKEGG
enrichKEGG KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
idType idType
simplify simplify method
viewKEGG viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway
fortify.compareClusterResult fortify
enrichMKEGG KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.
bitr_kegg bitr_kegg
bitr bitr
merge_result merge_result
plot plot method
download.KEGG download.KEGG
dropGO dropGO
getGOLevel get GOIDs at a specific level
Gff2GeneTable Gff2GeneTable
GSEA GSEA
groupGOResult-class Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
compareClusterResult-class Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
gseGO gseGO
compareCluster Compare gene clusters functional profile
gseKEGG gseKEGG
read.gmt read.gmt
DataSet Datasets gcSample contains a sample of gene clusters.
dotplot,compareClusterResult-method dotplot
go2ont go2ont
go2term go2term
gofilter gofilter
groupGO Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.
plotting.clusterProfile plotting-clusterProfile
plotGOgraph plotGOgraph
enrichDAVID enrichDAVID
enricher enricher
search_kegg_organism search_kegg_organism
No Results!

Last year downloads

Details

Type Package
VignetteBuilder knitr
License Artistic-2.0
URL http://guangchuangyu.github.io/clusterProfiler
BugReports https://github.com/GuangchuangYu/clusterProfiler/issues
Packaged NA
biocViews Annotation, Clustering, GeneSetEnrichment, GO, KEGG, MultipleComparison, Pathways, Reactome, Visualization
RoxygenNote 5.0.1

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/clusterProfiler)](http://www.rdocumentation.org/packages/clusterProfiler)