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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.