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

## Documentation for package ‘clusterProfiler’ version 3.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
bitr | bitr
bitr_kegg | bitr_kegg
buildGOmap | buildGOmap
clusterProfiler | 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.
compareCluster | Compare gene clusters functional profile
compareClusterResult-class | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
DataSet | Datasets gcSample contains a sample of gene clusters.
dotplot-method | dotplot
download.KEGG | download.KEGG
dropGO | dropGO
enrichDAVID | enrichDAVID
enricher | enricher
enrichGO | GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
enrichKEGG | KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
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.
fortify.compareClusterResult | fortify
gcSample | Datasets gcSample contains a sample of gene clusters.
getGOLevel | get GOIDs at a specific level
Gff2GeneTable | Gff2GeneTable
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.
groupGOResult-class | Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
GSEA | GSEA
gseGO | gseGO
gseKEGG | gseKEGG
gseMKEGG | gseMKEGG
idType | idType
kegg_species | Datasets gcSample contains a sample of gene clusters.
merge_result | merge_result
plot | plot method
plot-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
plot-method | plot method
plotGOgraph | plotGOgraph
plotting.clusterProfile | plotting-clusterProfile
read.gmt | read.gmt
search_kegg_organism | search_kegg_organism
show-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
show-method | Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
simplify | simplify method
simplify-method | simplify method
summary-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
viewKEGG | viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway