Examples
========

The example notebooks are available in the :ref:`Example Notebooks <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