iSubpathwayMiner-package | The iSubpathwayMiner package |
expandNode | Expand nodes according to the type of nodes |
filterNode | filter node according to node type |
gene2ec | The variables in the environment variable k2ri of the system |
gene2ko | The variables in the environment variable k2ri of the system |
getBackground | Get the background |
getEnzymeFromGene | Map between identifiers |
getEnzymeFromKGene | Map between identifiers |
getEnzymeFromSymbol | Map between identifiers |
getExample | Get a set of components |
getGeneFromEnzyme | Map between identifiers |
getGeneFromKGene | Map between identifiers |
getGeneFromKO | Map between identifiers |
getGeneFromPathway | Map between identifiers |
getGeneFromSymbol | Map between identifiers |
getKcSubiGraph | Mine subpathways |
getKGeneFromEnzyme | Map between identifiers |
getKGeneFromGene | Map between identifiers |
getKGeneFromKO | Map between identifiers |
getKGeneFromPathway | Map between identifiers |
getKGeneFromSymbol | Map between identifiers |
getKOFromGene | Map between identifiers |
getKOFromKGene | Map between identifiers |
getKOFromSymbol | Map between identifiers |
getMetabolicCOCOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicCOCOGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicCOCOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicCOCOUGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECCOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECCOGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECCOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECCOUGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECECEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECECGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECECUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicECECUGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicGEGEEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicGEGEUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicGraph | Convert metabolic pathways to graphs |
getMetabolicKOCOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOCOGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOCOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOCOUGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOKOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOKOGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOKOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getMetabolicKOKOUGraph | Get pathway graphs using the combination of graph conversion functions |
getNodeLabel | Get new node labels according to names attributes of graph |
getNonMetabolicGEGEEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicGEGEUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicGraph | Convert non-metabolic pathways to directed graphs |
getNonMetabolicKOCOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOCOGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOCOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOCOUGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOKOEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOKOGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOKOUEMGraph | Get pathway graphs using the combination of graph conversion functions |
getNonMetabolicKOKOUGraph | Get pathway graphs using the combination of graph conversion functions |
getOrgAndIdType | Get the type of organism and identifier in the current environment variable |
getOrgIdFromOrgName | Map between identifiers |
getOrgNameFromOrgId | Map between identifiers |
getPathway | Convert KGML files to a list variable in R |
getPathwayFromGene | Map between identifiers |
getPathwayFromKGene | Map between identifiers |
getPrioBackground | Get the conservative background |
getSimpleGraph | Convert multiple graphs to simple graphs |
getSymbolFromEnzyme | Map between identifiers |
getSymbolFromGene | Map between identifiers |
getSymbolFromKGene | Map between identifiers |
getSymbolFromKO | Map between identifiers |
getUGraph | Convert pathways to undirected graphs |
identifyGraph | Annotate a set of components to pathway graphs and identify statistically significantly enriched pathway graphs |
identifyTopo | Topology-based pathway analysis of gene sets |
importPathway | Update or import pathway files |
initializeK2ri | initialize environment k2ri |
iSubpathwayMiner | The iSubpathwayMiner package |
k2ri | The variables in the environment variable k2ri of the system |
keggGene2gene | The variables in the environment variable k2ri of the system |
loadK2ri | Load and save the environment variable k2ri of the system |
mapNode | Map current organism-specific gene identifiers to nodes in pathway graphs |
mergeNode | Merge nodes with the same names |
metabolicEC | The variables in the environment variable k2ri of the system |
metabolicKO | The variables in the environment variable k2ri of the system |
nonMetabolicKO | The variables in the environment variable k2ri of the system |
plotAnnGraph | Visualize annotated pathway graphs |
plotGraph | visualize a pathway graph |
printGraph | Print the results of graph annotation and identification |
printTopo | Print the results of topology-based pathway analysis of gene sets |
sampleComponent | Generate a random component set |
saveK2ri | Load and save the environment variable k2ri of the system |
simplifyGraph | Simplify pathways to gene product graphs or compound graphs |
updateCompound | Update compound identifiers |
updateOrgAndIdType | Update the organism and the type of gene identifier |
updatePathway | Update or import pathway files |
updateTaxonomy | Update taxonomy |