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Welcome to MCube's documentation!
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.. image:: figures/sticker.png
   :height: 128px
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   :alt: Sticker
   :target: https://github.com/YangLabHKUST/MCube

The R package ``MCube`` (`GitHub repository <https://github.com/YangLabHKUST/MCube>`_) implements the methods in the `MMM paper <https://doi.org/10.1073/pnas.2503952122>`_.
**MMM**, standing for the **Mixture of Mixed Models**,
is a unified framework for the statistical identification of cell-type-specific spatially variable genes (SVGs) in spatial transcriptomic (ST) studies.

MMM's effectiveness stems from our innovations in model and algorithm design:

* Beginning with the raw count data, MMM uses a **log-mixture structure** to account for cell type composition while simultaneously correcting for the spot and platform effects between ST and single‐cell RNA sequencing (scRNA-seq) data.
* The **mixed-effects model** decomposes the cell-type-specific gene expression in ST data into three components: the average gene expression of the same cell type obtained from scRNA-seq data, spatial variations, and non-spatial variations.
* The statistical significance of spatial variations is then examined using a powerful **non-parametric test** capable of detecting diverse spatial patterns.

On this tutorial website, we provide guidelines for using ``MCube`` along with real data analysis examples.
The source code for building the website can be found at https://github.com/statwangz/MCube-tutorial.

Contents
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.. toctree::
   :maxdepth: 2

   installation.rst
   usage.rst
   analysis/index.rst
   RCTD/index.rst

Reference
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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.
   | *Proceedings of the National Academy of Sciences of the United States of America*, 2025.
   | `DOI: 10.1073/pnas.2503952122 <https://doi.org/10.1073/pnas.2503952122>`_

Development
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The R package ``MCube`` is developed and maintained by `Zhiwei Wang <https://sites.google.com/view/statwangz>`_.

Contact
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Please feel free to contact `Zhiwei Wang <zhiwei.wang@connect.ust.hk>`_, `Prof. Hongyu Zhao <hongyu.zhao@yale.edu>`_,
`Prof. Zhixiang Lin <zhixianglin@cuhk.edu.hk>`_, or `Prof. Can Yang <macyang@ust.hk>`_ if any inquiries.