Reference

Protein complex overlap analysis
testConnectivity()	Assess connectivity of a graph on a set of node IDs
Protein domain association analysis
testDomainAssociation()	PFAM domain-domain association analysis
Protein structure visualization
viewPDB()	View a protein structure from PDB
Network visualization
plotGraph()	Plot a graph
Network utilities
joinNetworks()	Join multiple networks around a target node ID
GraphFrames backend
graph2graphframe()	Representation of BioPlex PPIs using a GraphFrames backend
graphframe2graph()	Convert a GraphFrames object to a graphNEL object