Table 1.
Comparison of network analysis tools.
| 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 | ✓ | ✓ | ✓ | ✓ | ||||||
BIT = MATLAB Bioinformatics Toolbox, BGL = MATLABBGL, BCT = Brain Connectivity Toolbox, NWB = Network Workbench, IN = Ingenuity Pathways Analysis, GG = GeneGo.