edges,KEGGPathway,ANY-method	KEGGPathway-class
edges,KEGGPathway-method	KEGGPathway-class
edges<-	KEGGPathway-class
edges<-,KEGGPathway-method	KEGGPathway-class
entryID<-	KEGGNode-class
entryID<-,KEGGEdge-method	KEGGEdge-class
entryID<-,KEGGNode-method	KEGGNode-class
expandKEGGNode	expandKEGGNode
expandKEGGPathway	expandKEGGPathway
getCategoryIndepKGMLurl	getKGMLurl
getComponent	KEGGGroup-class
getComponent,KEGGGroup-method	KEGGGroup-class
getComponent,KEGGNode-method	KEGGNode-class
getDisplayName	getDisplayName-methods
getDisplayName,graph-method	getDisplayName-methods
getDisplayName,KEGGNode-method	getDisplayName-methods
getDisplayName-methods	getDisplayName-methods
getEntryID	getEntryID-methods
getEntryID,KEGGEdge-method	getEntryID-methods
getEntryID,KEGGNode-method	getEntryID-methods
getEntryID,list-method	getEntryID-methods
getEntryID-methods	getEntryID-methods
getKEGGedgeData	getKEGGnodeData
getKEGGgeneLink	getKEGGgeneLink-methods
getKEGGgeneLink,character-method	getKEGGgeneLink-methods
getKEGGgeneLink-methods	getKEGGgeneLink-methods
getKEGGID	getKEGGID-methods
getKEGGID,KEGGNode-method	getKEGGID-methods
getKEGGID-methods	getKEGGID-methods
getKEGGnodeData	getKEGGnodeData
getKGMLurl	getKGMLurl
getName	getName-methods
getName,KEGGEdge-method	KEGGEdge-class
getName,KEGGEdgeSubType-method	KEGGEdgeSubType-class
getName,KEGGEdgeSubtype-method	getName-methods
getName,KEGGNode-method	getName-methods
getName,KEGGPathway-method	KEGGPathway-class
getName,KEGGPathwayInfo-method	getName-methods
getName,KEGGReaction-method	KEGGReaction-class
getName-methods	getName-methods
getNamedElement	getNamedElement
getPathwayInfo	getPathwayInfo-methods
getPathwayInfo,KEGGPathway-method	getPathwayInfo-methods
getPathwayInfo-methods	getPathwayInfo-methods
getProduct	KEGGReaction-class
getProduct,KEGGReaction-method	KEGGReaction-class
getReactions	getReactions-methods
getReactions,KEGGPathway-method	getReactions-methods
getReactions-methods	getReactions-methods
getRgraphvizEdgeNames	getRgraphvizEdgeNames
getSubstrate	KEGGReaction-class
getSubstrate,KEGGReaction-method	KEGGReaction-class
getSubtype	getSubtype-methods
getSubtype,graph-method	getSubtype-methods
getSubtype,KEGGEdge-method	getSubtype-methods
getSubtype-methods	getSubtype-methods
getTitle	getTitle-methods
getTitle,KEGGPathway-method	KEGGPathway-class
getTitle,KEGGPathwayInfo-method	KEGGPathwayInfo-class
getTitle-methods	getTitle-methods
getType	getType-methods
getType,KEGGEdge-method	getType-methods
getType,KEGGNode-method	getType-methods
getType,KEGGReaction-method	getType-methods
getType-methods	getType-methods
getValue	getValue-methods
getValue,KEGGEdgeSubType-method	KEGGEdgeSubType-class
getValue,KEGGEdgeSubtype-method	getValue-methods
getValue-methods	getValue-methods
graphDensity	graphDensity
isHomoList	isHomoList
KEGGEdge-class	KEGGEdge-class
KEGGEdgeSubtype	KEGGEdgeSubtype
KEGGEdgeSubType-class	KEGGEdgeSubType-class
KEGGEdgeType	KEGGEdgeSubtype
KEGGGraphics-class	KEGGGraphics-class
KEGGgraphLegend	plotKEGGgraph
KEGGGroup-class	KEGGGroup-class
KEGGNode-class	KEGGNode-class
KEGGNodeType	KEGGEdgeSubtype
KEGGPathway-class	KEGGPathway-class
KEGGpathway2Graph	KEGGpathway2Graph
KEGGpathway2reactionGraph	KEGGpathway2reactionGraph
KEGGPathwayInfo-class	KEGGPathwayInfo-class
KEGGReaction-class	KEGGReaction-class
kgmlFileName2PathwayName	kgmlFileName2PathwayName
kgmlNonmetabolicName2MetabolicName	getKGMLurl
mergeGraphs	mergeGraphs
mergeKEGGgraphs	mergeKEGGgraphs
name<-	KEGGNode-class
name<-,KEGGNode-method	KEGGNode-class
neighborhood	neighborhood
nodes,KEGGPathway-method	KEGGPathway-class
nodes<-,KEGGPathway,ANY-method	KEGGPathway-class
parseEntry	parseEntry
parseGraphics	parseGraphics
parseKGML	parseKGML
parseKGML2Graph	parseKGML2Graph
parseKGMLexpandMaps	parseKGMLexpandMaps
parsePathwayInfo	parsePathwayInfo
parseReaction	parseReaction
parseRelation	parseRelation
parseSubType	parseSubType
plotKEGGgraph	plotKEGGgraph
pvalue2asterisk	pvalue2asterisk
queryKEGGsubgraph	queryKEGGsubgraph
randomSubGraph	randomSubGraph
retrieveKGML	getKGMLurl
setKEGGedgeData	getKEGGnodeData
setKEGGnodeData	getKEGGnodeData
show,KEGGEdge-method	KEGGEdge-class
show,KEGGEdgeSubType-method	KEGGEdgeSubType-class
show,KEGGNode-method	KEGGNode-class
show,KEGGPathway-method	KEGGPathway-class
show,KEGGPathwayInfo-method	KEGGPathwayInfo-class
show,KEGGReaction-method	KEGGReaction-class
splitKEGGgroup	splitKEGGgroup
subGraphByNodeType	subGraphByNodeType
subKEGGgraph	subKEGGgraph
subtypeDisplay	subtypeDisplay-methods
subtypeDisplay,graph-method	subtypeDisplay-methods
subtypeDisplay,KEGGEdge-method	subtypeDisplay-methods
subtypeDisplay,KEGGEdgeSubType-method	subtypeDisplay-methods
subtypeDisplay-methods	subtypeDisplay-methods
top	top
translateGeneID2KEGGID	translateKEGGID2GeneID
translateKEGG2GeneID	translateKEGGID2GeneID
translateKEGGgraph	translateKEGGgraph
translateKEGGID2GeneID	translateKEGGID2GeneID
