I would like to know what libraries/modules are used by BioStar members for large scale analysis of networks (for example PPI, DDI etc). I am looking for a module that can provide various functions to calculate network algorithms and network properties. Since I have to deal with thousands of networks, Cytoscape via GUI will not be a feasible option. I think a command line version of version of the Cytoscape plugin NetworkAnalyzer will be a good start.
I know about Bio::Network at Bioperl, but the functionality is very limited. Networkx have some of the implementation of network algorithms from a graph theory perspective, but not as extensive as in NetworkAnalyzer.
Looking forward for your suggestions.