- Network Inference by Reverse-engineering NIR
- Mode-of-action by Network Inference MNI
- Time Series Network Identification TSNI-integral
- Time Series Network Identification TSNI
- MANTRA - Mode of Action by Network Analysis
- NETVIEW - Gene Networks in Human and Mouse
- DINA - DIfferential Network Anlysis
- DINA is a tool able to identify sets of genes which are significantly co-regulated only in specific conditions, but not in others.