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MMCCI
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Multi-platform, Multi-sample Cell-Cell Interaction Integrative Analysis of Single Cell and Spatial Data
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**MMCCI** is an open-source Python package for analyzing cell–cell interaction data from different CCI tools. 
This documentation provides an overview, installation guidelines, API reference, and usage examples.

Source code is available on `GitHub <https://github.com/GenomicsMachineLearning/MMCCI>`_.
Issues can be reported on the `GitHub issue tracker <https://github.com/GenomicsMachineLearning/MMCCI/issues>`_.

.. image:: https://raw.githubusercontent.com/GenomicsMachineLearning/MMCCI/refs/heads/main/docs/images/analyses_pipeline.png
    :alt: MMCCI title figure
    :width: 800px
    :align: center
    :target: https://doi.org/10.1101/2024.02.28.582639

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MMCCI's key applications
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MMCCI allows users to integrate multiple CCI results together, both:

   1. Samples from a single platform (eg. Visium)
   2. Samples from multiple platforms (eg. Visium, Xenium and CosMx, and CODEX)

MMCCI provides multiple useful analyses that can be run on the integrated networks or from a single sample:

   1. Network comparison between groups with permutation testing
   2. Clustering of LR pairs with similar networks
   3. Clustering of spots/cells with similar interaction scores
   4. Sender-receiver LR querying
   5. GSEA pathway analysis


.. toctree::
    :caption: General
    :maxdepth: 2
    :hidden:

    getting_started
    api

.. toctree::
    :caption: Examples
    :maxdepth: 2
    :hidden:

    notebooks/brain_aging_example
    notebooks/melanoma_example
    notebooks/loading_CCI_results

.. |PyPI| image:: https://img.shields.io/pypi/v/mmcci.svg
    :target: https://pypi.org/project/mmcci/
    :alt: PyPI

.. |Docs| image:: https://img.shields.io/readthedocs/mmcci
    :target: https://mmcci.readthedocs.io/en/stable/
    :alt: Documentation

.. |Downloads| image:: https://pepy.tech/badge/mmcci
    :target: https://pepy.tech/project/mmcci
    :alt: Downloads