Tutorial
========

.. note::
   This tutorial will walk you through a complete scHopfield analysis using a hematopoiesis dataset.
   Coming soon!

Overview
--------

This tutorial demonstrates:

1. Loading and preprocessing single-cell RNA-seq data
2. Computing RNA velocity with scVelo
3. Fitting sigmoid functions to gene expression
4. Inferring gene regulatory networks
5. Computing and analyzing energy landscapes
6. Network topology analysis
7. Stability analysis with Jacobians
8. Visualizing results
9. Simulating perturbations

Dataset
-------

We'll use a hematopoietic differentiation dataset with the following cell types:

- Hematopoietic Stem Cells (HSC)
- Multipotent Progenitors (MPP)
- Common Myeloid Progenitors (CMP)
- Granulocyte-Monocyte Progenitors (GMP)
- Megakaryocyte-Erythroid Progenitors (MEP)

Prerequisites
-------------

Before starting, ensure you have:

- scHopfield installed (see :doc:`installation`)
- scVelo for RNA velocity computation
- A single-cell dataset with spliced/unspliced counts

Step-by-Step Analysis
----------------------

Coming soon! This section will include:

- Data loading and quality control
- RNA velocity computation
- Sigmoid fitting and network inference
- Energy landscape analysis
- Network topology analysis
- Jacobian stability analysis
- Visualization examples
- Perturbation simulations

See Also
--------

- :doc:`quickstart` - Quick start guide
- :doc:`examples` - Example notebooks
- :doc:`api/tools` - API reference