SDEvelo Documentation
===============================

.. image:: _static/sde_flow.png
   :alt: SDEvelo Flow Chart
   :align: center

Welcome to the **SDEvelo** documentation! SDEvelo represents a significant advancement in single-cell RNA sequencing (scRNA-seq) and sequence-based spatial transcriptomics (ST) analysis.

.. toctree::
   :maxdepth: 2
   :caption: Contents

   overview
   installation


===============================
Key Features
===============================

- **Multivariate stochastic modeling** of transcriptional dynamics
- **Cell-specific latent time estimation**
- **Versatile Compatibility**: Applicable to both scRNA-seq and sequencing-based spatial transcriptomics data
- **Computationally Scalable**

===============================
Quick Start
===============================

To install SDEvelo, use `pip`:

.. code-block:: bash

    pip install sdevelo

For more detailed usage instructions, see the :doc:`Installation <installation>` section.

===============================
Tutorials
===============================

Explore our comprehensive tutorials to get started with SDEvelo:

.. toctree::
   :maxdepth: 1
   :caption: Tutorials

   tutorials/simulation
   tutorials/demo_HCC1
   tutorials/demo_HCC2
   tutorials/demo_reprogramming
   tutorials/demo_erythroid
   tutorials/demo_pbmc