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Table 1 Comparison of features in NetWalker, Cytoscape, BiologicalNetworks and VisANT

From: NetWalker: a contextual network analysis tool for functional genomics

  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
  1. Unique features of NetWalker are in bold.