Introduction | Installation | Installation of Python and its dependencies | Example Data Set Description | Load the data | Transform the data to the required input format | Create the individual layers data structure from the molecular data | Create inter-layer connections data structure | Create drug-target interaction data structure | Check input data structures | Run the complete pipeline | Run the individual pipeline steps | Step 1: Compute correlation matrices | Step 2: Generate individual graphs | Step 3: Combine graphs | Step 4: Identify drug targets and their edges | Step 5: Calculate integrated interaction score | Step 6: Generate differential graph | Step 7: Calculate differential drug response score | References

Installation | In brief and quick start | Introduction | Solving the ODE model to generate variable values of interest | Calculating the Jacobian matrix | Computing all feedback loops and useful functions for loop search | Computing feedback loops over multiple sets of variable values of interest | Comparing two loop lists | References