Examples

The example notebooks are available in the Example Notebooks section at the top of this documentation. They demonstrate scHopfield’s capabilities on a hematopoiesis dataset (Paul et al. 2015) and cover:

• Getting started: data loading, sigmoid fitting, network inference

• Energy analysis: computing and visualising energy landscapes

• Network analysis: centrality metrics, eigenanalysis, GRN visualization

• Stability analysis: Jacobian computation, eigenvalue spectra

• Perturbation analysis: in-silico gene knockouts and ODE simulation