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.

AuthorGuangchuang Yu [aut, cre], Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version3.2.11
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_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

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

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