Tools and Resources
The Network Zoo:
Regulatory Network Reconstruction Algorithms:
PANDA: Passing Attributes between Networks for Data Assimilation
LIONESS: Linear Interpolation to Obtain Estimates for Single Samples (with Marieke Kuijjer)
PUMA: PANDA Using MicroRNA Associations (with Marieke Kuijjer)
SPIDER: Seeding PANDA Interactions to Derive Epigenetic Regulation (with Abhijeet Sonawane)
(Coming Soon) EGRET: Estimating the Genetic Regulatory Effect on TFs (with John Platig)
Related Network Analysis Algorithms:
ALPACA : ALtered Partitions Across Community Architectures (developed by Megha Padi)
CONDOR: COmplex Network Description Of Regulators (developed by John Platig)
MONSTER: MOdeling Network State Transitions from Expression and Regulatory data (with Dan Schlauch)
Additional Resources and Code can also be found on the netZoo github repository.
Additional Network Resources:
Gene Ontology Tools: