Welcome to stGP's documentation!
=================================

**stGP** is a spatiotemporal gene program modeling framework for spatial
transcriptomics. It decomposes target-cell gene expression across tissue
sections into latent gene programs, cell-level program activities, spatially
smooth residual fields, and temporal effects.

.. image:: figures/overview.png
   :align: center
   :alt: stGP model overview

This tutorial website provides runnable notebook examples for applying ``stGP``
to aging brain and injured kidney spatial transcriptomics studies. The upstream
``stGP`` source code is available from the `YangLabHKUST/stGP GitHub repository
<https://github.com/YangLabHKUST/stGP>`_, and the tutorial website source is
available from https://github.com/Jamesyu420/stGP-tutorial.

Contents
========

.. toctree::
   :maxdepth: 2

   installation.rst
   tutorials/index.rst

Reference
=========

If you find ``stGP`` or any of the source code in the repository useful for your
work, please cite:

   Characterizing dynamic tissue architectures by identifying cell-type-specific
   spatiotemporal gene programs with stGP.

   Baichen Yu, Ziyue Tan, Xiaomeng Wan, Hansheng Wang, and Can Yang.

   Working paper, 2026.

Development
===========

The software is developed and maintained by `Baichen Yu <mailto:mabyu@ust.hk>`_.

Contact
=======

Please feel free to contact `Baichen Yu <mailto:mabyu@ust.hk>`_ or `Prof. Can
Yang <mailto:macyang@ust.hk>`_ if any inquiries.