append_kegg_category    append_kegg_category
bitr                    bitr
bitr_kegg               bitr_kegg
browseKEGG              browseKEGG
compareCluster          Compare gene clusters functional profile
DataSet                 Datasets gcSample contains a sample of gene
                        clusters.
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.
enrichPC                enrichPC
enrichWP                enrichWP
get_wp_organisms        get_wp_organism
getPPI                  getPPI
getTaxID                getTaxID
getTaxInfo              getTaxInfo
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
gsePC                   gsePC
gseWP                   gseWP
gson_GO                 gson_KEGG
gson_GO_local           Build a gson object that annotate Gene Ontology
gson_KEGG               gson_KEGG
gson_KEGG_mapper        Build KEGG annotation for novel species using
                        KEGG Mapper
gson_WP                 gson_WP
idType                  idType
interpret               Interpret Enrichment Results Using LLMs
interpret_agent         Interpret enrichment results using a
                        multi-agent pipeline (Deep Mode)
interpret_hierarchical
                        Interpret enrichment results using a
                        hierarchical strategy
ko2name                 ko2name
merge_result            merge_result
plot.interpretation     plot
plotGOgraph             plotGOgraph
read.gmt.pc             read.gmt.pc
search_kegg_organism    search_kegg_organism
simplify                simplify method
uniprot_get             uniprot_get
