clusterProfiler: 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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")
AuthorGuangchuang Yu [aut, cre], Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Bioconductor views Annotation Clustering GO GeneSetEnrichment KEGG MultipleComparison Pathways Reactome Visualization
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version3.4.0
https://guangchuangyu.github.io/clusterProfiler

View on Bioconductor

Functions

bitr Man page
bitr_kegg Man page
browseKEGG Man page
buildGOmap Man page
clusterProfiler Man page
clusterProfiler-package Man page
compareCluster Man page
compareClusterResult-class Man page
DataSet Man page
dotplot,compareClusterResult,ANY-method Man page
dotplot,compareClusterResult-method Man page
download_KEGG Man page
dropGO Man page
enrichDAVID Man page
enricher Man page
enrichGO Man page
enrichKEGG Man page
enrichMKEGG Man page
fortify.compareClusterResult Man page
gcSample Man page
getGOLevel Man page
Gff2GeneTable Man page
go2ont Man page
go2term Man page
gofilter Man page
groupGO Man page
groupGOResult-class Man page
GSEA Man page
gseGO Man page
gseKEGG Man page
gseMKEGG Man page
idType Man page
KEGG_path2extid Man page
kegg_species Man page
merge_result Man page
plot Man page
plot,compareClusterResult,ANY-method Man page
plot,compareClusterResult-method Man page
plotGOgraph Man page
plotting.clusterProfile Man page
read.gmt Man page
search_kegg_organism Man page
show,compareClusterResult-method Man page
show,groupGOResult-method Man page
simplify Man page
simplify,compareClusterResult-method Man page
simplify,enrichResult-method Man page
summary,compareClusterResult-method Man page
viewKEGG Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/00-AllClasses.R R/AllGenerics.R R/DOSE.R R/GFFparser.R R/GMT.R R/accessor.R R/bitr.R R/buildGOmap.R R/clusterProfiler-package.R R/compareCluster.R R/dotplot.R R/enrichDAVID.R R/enrichGO.R R/enrichKEGG.R R/enrichMKEGG.R R/enricher.R R/go-utilities.R R/gofilter.R R/groupGO.R R/gseAnalyzer.R R/kegg-utilities.R R/plotGOgraph.R R/simplify.R R/utilities.R R/zzz.R
build
build/vignette.rds
data
data/gcSample.rda
data/kegg_species.rda
inst
inst/CITATION
inst/doc
inst/doc/clusterProfiler.R
inst/doc/clusterProfiler.Rmd
inst/doc/clusterProfiler.html
inst/extdata
inst/extdata/c5.cc.v5.0.entrez.gmt
man
man/DataSet.Rd man/GSEA.Rd man/Gff2GeneTable.Rd man/KEGG_path2extid.Rd man/bitr.Rd man/bitr_kegg.Rd man/browseKEGG.Rd man/buildGOmap.Rd man/clusterProfiler-package.Rd man/compareCluster.Rd man/compareClusterResult-class.Rd man/dotplot-methods.Rd man/download_KEGG.Rd man/dropGO.Rd man/enrichDAVID.Rd man/enrichGO.Rd man/enrichKEGG.Rd man/enrichMKEGG.Rd man/enricher.Rd man/fortify.Rd man/getGOLevel.Rd man/go2ont.Rd man/go2term.Rd man/gofilter.Rd man/groupGO.Rd man/groupGOResult-class.Rd man/gseGO.Rd man/gseKEGG.Rd man/gseMKEGG.Rd man/idType.Rd man/merge_result.Rd man/plot-methods.Rd man/plotGOgraph.Rd man/plotting.clusterProfile.Rd man/read.gmt.Rd man/search_kegg_organism.Rd man/simplify-methods.Rd man/viewKEGG.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test-bitr.R
vignettes
vignettes/clusterProfiler.Rmd
vignettes/clusterProfiler.bib
vignettes/figures
vignettes/figures/browseKEGG.png
vignettes/figures/cnetplot.png
vignettes/figures/enrichMap.png
vignettes/figures/hsa04110_pathview.png
vignettes/nature.csl
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