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.

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, and the tutorial website source is available from https://github.com/Jamesyu420/stGP-tutorial.

Contents

• Installation
  • Build the tutorial documentation locally
• Tutorial notebooks
  • Human aging DLPFC
  • Mouse aging brain
  • Mouse injured kidney

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.

Contact

Please feel free to contact Baichen Yu or Prof. Can Yang if any inquiries.