Table 1 Comparison of features in NetWalker, Cytoscape, BiologicalNetworks and VisANT
From: NetWalker: a contextual network analysis tool for functional genomics
| Â | NetWalker | Cytoscape | BiologicalNetworks | VisANT |
|---|---|---|---|---|
Pre-compiled interactome knowledgebase | NetWalker Interactome Knowledgebase | No central knowledgebase, can import external interaction sets | IntegromeDB | Predictome |
Dataset import and processing | Yes | Yes | Yes | No |
Clustering and heatmaps | Yes | plugin | Yes | No |
Network building with genes of interest | GeneConnector | plugins | Shortest paths, common interactors, filtering | No |
Pre-defined canonical pathways | No | No | Yes | No |
Whole distribution-based network scoring method | NetWalk | No | No | No |
Unique network integration/analysis method | NetWalk, FunWalk, EF Tables, GeneConnector, FunTable | ActiveModules, other plugins | No | GOTEA, NMEA |
Functional enrichment analysis | Hypergeometric, FunWalk | BiNGO plugin | Fisher’s Exact Probability | GOTEA, NMEA |
Analyses/visualizations of sequence/structure data | No | No | Yes | No |
Support for non-mammalian species data/networks | No | Yes | Yes | Yes |
Interoperability with R | Yes | No | No | No |