rBiopaxParser-package	rBiopaxParser-package
addBiochemicalReaction	addBiochemicalReaction
addBiopaxInstance	addBiopaxInstance
addBiopaxInstances	addBiopaxInstances
addControl	addControl
addhash	addhash
addns	addns
addPathway	addPathway
addPathwayComponents	addPathwayComponents
addPhysicalEntity	addPhysicalEntity
addPhysicalEntityParticipant	addPhysicalEntityParticipant
addPropertiesToBiopaxInstance	addPropertiesToBiopaxInstance
biopax	biopax
calcGraphOverlap	calcGraphOverlap
checkValidity	checkValidity
CLASS_INHERITANCE_BP2	CLASS_INHERITANCE_BP2
CLASS_INHERITANCE_BP3	CLASS_INHERITANCE_BP3
CLASS_PROPERTIES_BP2	CLASS_PROPERTIES_BP2
CLASS_PROPERTIES_BP3	CLASS_PROPERTIES_BP3
colorGraphNodes	colorGraphNodes
combineNodes	combineNodes
createBiopax	createBiopax
DATABASE_BIOPAX	DATABASE_BIOPAX
diffGraphs	diffGraphs
downloadBiopaxData	downloadBiopaxData
generateNewUniqueID	generateNewUniqueID
getClassProperties	getClassProperties
getInstanceClass	getInstanceClass
getInstanceProperty	getInstanceProperty
getNeighborhood	getNeighborhood
getReferencedIDs	getReferencedIDs
getReferencingIDs	getReferencingIDs
getSubClasses	getSubClasses
getSuperClasses	getSuperClasses
getXrefAnnotations	getXrefAnnotations
hasProperty	hasProperty
internal_checkArguments	internal_checkArguments
internal_generateXMLfromBiopax	internal_generateXMLfromBiopax
internal_getBiopaxModelAsDataFrame	internal_getBiopaxModelAsDataFrame
internal_NrOfXMLNodes	internal_NrOfXMLNodes
internal_propertyListToDF	internal_propertyListToDF
internal_resolvePhysicalEntityParticipant	internal_resolvePhysicalEntityParticipant
internal_XMLInstance2DF	internal_XMLInstance2DF
intersectGraphs	intersectGraphs
isOfClass	isOfClass
isOfNamespace	isOfNamespace
layoutRegulatoryGraph	layoutRegulatoryGraph
listComplexComponents	listComplexComponents
listInstances	listInstances
listInteractionComponents	listInteractionComponents
listPathwayComponents	listPathwayComponents
listPathways	listPathways
mergePathways	mergePathways
pathway2AdjacancyMatrix	pathway2AdjacancyMatrix
pathway2Geneset	pathway2Geneset
pathway2RegulatoryGraph	pathway2RegulatoryGraph
plotRegulatoryGraph	plotRegulatoryGraph
print.biopax	print.biopax
rBiopaxParser	rBiopaxParser-package
readBiopax	readBiopax
removeInstance	removeInstance
removeNodes	removeNodes
removeProperties	removeProperties
selectInstances	selectInstances
splitComplex	splitComplex
striphash	striphash
stripns	stripns
transitiveClosure	transitiveClosure
transitiveReduction	transitiveReduction
unfactorize	unfactorize
uniteGraphs	uniteGraphs
writeBiopax	writeBiopax
