Files in rBiopaxParser

Parses BioPax files and represents them in R

README.md R/parseBiopax.R R/helperFunctions.R R/rBiopaxParser-package.R R/pathway2Graph.R R/selectBiopax.R R/modifyBiopax.R R/downloadBiopaxData.R R/biopax2Classes.R R/visualizeBiopax.R R/writeBiopax.R vignettes/biopax2classgraph.pdf vignettes/mergedpw.pdf vignettes/biopaxsimple.pdf vignettes/segclock.pdf vignettes/wntplot.pdf man/CLASS_INHERITANCE_BP2.Rd man/CLASS_INHERITANCE_BP3.Rd man/getNeighborhood.Rd man/biopax.Rd man/pathway2AdjacancyMatrix.Rd man/isOfNamespace.Rd man/internal_propertyListToDF.Rd man/addBiopaxInstances.Rd man/checkValidity.Rd man/getXrefAnnotations.Rd man/DATABASE_BIOPAX.Rd man/generateNewUniqueID.Rd man/writeBiopax.Rd man/addBiochemicalReaction.Rd man/getParticipants.Rd man/colorGraphNodes.Rd man/splitComplex.Rd man/addPhysicalEntityParticipant.Rd man/addPhysicalEntity.Rd man/calcGraphOverlap.Rd man/transitiveClosure.Rd man/getSuperClasses.Rd man/pathway2Graph.Rd man/listInteractionComponents.Rd man/listPathways.Rd man/selectInstances.Rd man/pathway2Geneset.Rd man/addBiopaxInstance.Rd man/getReferencingIDs.Rd man/plotRegulatoryGraph.Rd man/listPathwayComponents.Rd man/internal_checkArguments.Rd man/addhash.Rd man/getInstanceProperty.Rd man/getSubClasses.Rd man/readBiopax.Rd man/CLASS_PROPERTIES_BP2.Rd man/intersectGraphs.Rd man/downloadBiopaxData.Rd man/addControl.Rd man/addPropertiesToBiopaxInstance.Rd man/isURL.Rd man/getInstanceClass.Rd man/isOfClass.Rd man/CLASS_PROPERTIES_BP3.Rd man/pathway2RegulatoryGraph.Rd man/unfactorize.Rd man/internal_getBiopaxModelAsDataFrame.Rd man/addPathway.Rd man/removeProperties.Rd man/layoutRegulatoryGraph.Rd man/print.biopax.Rd man/addPathwayComponents.Rd man/listInstances.Rd man/listComplexComponents.Rd man/diffGraphs.Rd man/internal_generateXMLfromBiopax.Rd man/uniteGraphs.Rd man/internal_XMLInstance2DF.Rd man/stripns.Rd man/mergePathways.Rd man/createBiopax.Rd man/removeDisconnectedParts.Rd man/transitiveReduction.Rd man/getReferencedIDs.Rd man/removeNodes.Rd man/internal_resolvePhysicalEntityParticipant.Rd man/hasProperty.Rd man/addns.Rd man/striphash.Rd man/getClassProperties.Rd man/rBiopaxParser-package.Rd man/internal_NrOfXMLNodes.Rd man/removeInstance.Rd man/combineNodes.Rd tests/runTests.R inst/doc/rBiopaxParserVignette.R inst/doc/rBiopaxParserVignette.pdf inst/unitTests/test_downloadBiopaxData.R inst/unitTests/test_helperFunctions.R inst/unitTests/test_biopax2Classes.R