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| background | The Background Genes. |
| cutoffAnn | Get the statistically significantly enriched pathways |
| dGraph | Directed graph list based on enzyme commission (EC) numbers constructed from KEGG metabolic pathways |
| ec2gene | A list that maps Enzyme Commission (EC) numbers to gene identifiers |
| gene2ec | A list that maps gene identifiers to Enzyme Commission (EC) numbers |
| gene2KO | A list that maps gene identifiers to KEGG Orthology (KO) |
| gene2path | A list that maps gene identifiers to KEGG pathway identifiers |
| getAexample | Get a set of genes |
| getAnn | Annotate a set of genes to pathways or sub-pathways based on enzyme commission (EC) |
| getDefaultBackground | Get the default background genes |
| getDefaultGraph | Get relationship between KEGG pathways and genes |
| getDefaultKOPathway | Get an identifier list of the default pathways based on KEGG Orthology (KO) |
| getDefaultKOUndirectedGraph | Get the default undirected graph based on KEGG Orthology |
| getDefaultMetabolicPathway | Get an identifier list of the default metabolic pathways |
| getDefaultUndirectedGraph | Get the default undirected graph based onenzyme commission (EC) numbers |
| getEnzymeFromGene | Get a list of enzymes from a list of genes |
| getGeneFromEnzyme | Get a list of genes from a list of enzymes |
| getGeneFromKO | Get a list of genes from a list of KOs |
| getGeneFromPathway | Get genes from pathways |
| getKcsmpAnn | Get the sub-pathways annotation and identification of metabolic network |
| getKcSubGraph | Mine sub-pathways |
| getKOAnn | Annotate a set of genes to sub-pathways by using KEGG Orthology (KO) |
| getKOFromGene | Get a list of KOs from a list of genes |
| getMpAnn | get annotation informations of metabolic pathways |
| getOrgAndIdType | Get the type of organism and identifier in the current environment variable |
| getPathwayFromGene | Get pathwaysfrom genes |
| getPathwayNameFromId | Get pathway name from identifier |
| gotoKEGG | Visualize pathways or sub-pathways through linking to the KEGG web site |
| ke2g | The environment variable of the system |
| keggpathid2name | The data that maps KEGG pathway identifiers to names |
| KO2gene | A list that maps KEGG Orthology (KO) to gene identifiers |
| KOuGraph | The undirected graph list based on KEGG Orthology (KO) identifiers constructed from KEGG pathways |
| kpidList | pathway identifier list based on KEGG Orthology (KO) |
| loadKe2g | ke2g environment function |
| mpidList | metabolic pathway identifier list |
| path2gene | A list that maps KEGG pathway identifiers to gene identifiers |
| plotAnn | Visualize pathways or sub-pathways based on enzyme commission (EC) numbers |
| plotKOAnn | Visualize pathways or sub-pathways based on KEGG Orthology (KO) |
| printAnn | Print the results of pathway annotation and identification |
| saveKe2g | ke2g environment function |
| uGraph | The undirected graph list based on enzyme commission (EC) numbers constructed from KEGG metabolic pathways |
| updateGraphs | Update graphs constructed from KEGG metabolic pathways |
| updateKOGraphs | Update graphs based on based on KEGG Orthology (KO) constructed from KEGG pathways |
| updateOrgAndIdType | Update the organism and the type of gene identifier |