MCube: Identifying cell-type-specific spatially variable genes with the Mixture of Mixed Models

Introduction

The R package MCube implements the methods in the MMM paper. MMM, standing for the Mixture of Mixed Models, is a unified framework for statistical identification of cell-type-specific spatially variable genes in spatial transcriptomic (ST) studies.

Installation

You can install the development version of MCube from GitHub with:

# install.packages("devtools")
devtools::install_github("YangLabHKUST/MCube")

Real data analysis

The code for reproducing the real data analysis results presented in our paper are available on the tutorial website (https://mcube-tutorial.readthedocs.io/):

• Visium human dorsolateral prefrontal cortex dataset
• Multiple adult mouse brain datasets from different sources
• Xenium human breast cancer dataset
• 3D Drosophila embryo model constructed from Stereo-seq dataset

Reference

If you find the MCube package or any of the source code in this repository useful for your work, please cite:

A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies.
Zhiwei Wang, Yeqin Zeng, Ziyue Tan, Yuheng Chen, Xinrui Huang, Hongyu Zhao, Zhixiang Lin, and Can Yang.
2025.

Development

The R package MCube is developed and maintained by Zhiwei Wang.

Contact

Please feel free to contact Zhiwei Wang, Prof. Hongyu Zhao, Prof. Zhixiang Lin, or Prof. Can Yang if any inquiries.