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Table 1 Comparison of network analysis tools.

From: Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks

Tool FUGA BIT BGL BCT NATbox igraph NeAT NWB IN GG
Interface MATLAB MATLAB MATLAB MATLAB R C/R/Python Web-based Java Java Java
User-defined networks
Curated pathway/network content: API        
Computational network reconstruction        
Statistical network analysis
Biological enrichment/annotation        
Expression analysis        
  1. BIT = MATLAB Bioinformatics Toolbox, BGL = MATLAB BGL, BCT = Brain Connectivity Toolbox, NWB = Network Workbench, IN = Ingenuity Pathways Analysis, GG = GeneGo.