graphite: GRAPH Interaction from pathway Topological Environment

Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.

Install the latest version of this package by entering the following in R:
AuthorGabriele Sales <>, Enrica Calura <>, Chiara Romualdi <>
Bioconductor views BioCarta GraphAndNetwork KEGG Network Pathways Reactome ThirdPartyClient
Date of publicationNone
MaintainerGabriele Sales <>

View on Bioconductor


as.list.DeprecatedPathwayList Man page
as.list.PathwayList Man page
biocarta Man page
buildPathway Man page
convertIdentifiers Man page
convertIdentifiers,DeprecatedPathwayList-method Man page
convertIdentifiers,PathwayList-method Man page
convertIdentifiers,Pathway-method Man page
cytoscapePlot Man page
DeprecatedPathwayList-class Man page
[,DeprecatedPathwayList-method Man page
[[,DeprecatedPathwayList-method Man page
$,DeprecatedPathwayList-method Man page
edges,Pathway,ANY-method Man page
humancyc Man page
kegg Man page
length,DeprecatedPathwayList-method Man page
length,PathwayList-method Man page
names,DeprecatedPathwayList-method Man page
names,PathwayList-method Man page
nci Man page
nodes,Pathway-method Man page
panther Man page
Pathway-class Man page
pathwayDatabases Man page
pathwayGraph Man page
PathwayList-class Man page
[,PathwayList-method Man page
[[,PathwayList-method Man page
$,PathwayList-method Man page
pathways Man page
Pathways-class Man page
plot,Pathway,ANY-method Man page
prepareSPIA Man page
prepareSPIA,DeprecatedPathwayList-method Man page
prepareSPIA,list-method Man page
prepareSPIA,PathwayList-method Man page
reactome Man page
runClipper Man page
runClipper,DeprecatedPathwayList-method Man page
runClipper,list-method Man page
runClipperMulti Man page
runClipper,PathwayList-method Man page
runClipper,Pathway-method Man page
runDEGraph Man page
runDEGraph,DeprecatedPathwayList-method Man page
runDEGraph,list-method Man page
runDEGraphMulti Man page
runDEGraph,PathwayList-method Man page
runDEGraph,Pathway-method Man page
runSPIA Man page
runTopologyGSA Man page
runTopologyGSA,DeprecatedPathwayList-method Man page
runTopologyGSA,list-method Man page
runTopologyGSAMulti Man page
runTopologyGSA,PathwayList-method Man page
runTopologyGSA,Pathway-method Man page

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.