DataSet                 Datasets gcSample contains a sample of gene
                        clusters.
GSEA                    GSEA
Gff2GeneTable           Gff2GeneTable
KEGG_path2extid         KEGG_path2extid
bitr                    bitr
bitr_kegg               bitr_kegg
browseKEGG              browseKEGG
buildGOmap              buildGOmap
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.
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.
dotplot,compareClusterResult-method
                        dotplot
download_KEGG           download_KEGG
dropGO                  dropGO
enrichDAVID             enrichDAVID
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.
enricher                enricher
fortify.compareClusterResult
                        fortify
getGOLevel              get GOIDs at a specific level
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.
gseGO                   gseGO
gseKEGG                 gseKEGG
gseMKEGG                gseMKEGG
idType                  idType
merge_result            merge_result
plot                    plot method
plotGOgraph             plotGOgraph
plotting.clusterProfile
                        plotting-clusterProfile
read.gmt                read.gmt
search_kegg_organism    search_kegg_organism
simplify                simplify method
viewKEGG                viewKEGG function is for visualize KEGG
                        pathways works with enrichResult object to
                        visualize enriched KEGG pathway
