multimodal-cci 1.2.2
A Python package for processing multi-modal CCI data
Requires Python: >=3.9

# MMCCI: Multimodal Cell-Cell Interaction Integrative Analysis of Single Cell and Spatial Data

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    <td>
      <b>Package</b>
    </td>
    <td>
      <a href="https://pypi.python.org/pypi/multimodal-cci/">
      <img src="https://img.shields.io/pypi/v/multimodal-cci.svg" alt="PyPI Version">
      </a>
      <a href="https://pepy.tech/project/multimodal-cci">
      <img src="https://static.pepy.tech/personalized-badge/multimodal-cci?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads"
        alt="PyPI downloads">
    </td>
  </tr>
  <tr>
    <td>
     <b>Paper</b>
    </td>
    <td>
      <a href="https://doi.org/10.1101/2023.05.14.540710"><img src="https://zenodo.org/badge/DOI/10.1101/2023.05.14.540710.svg"
        alt="DOI"></a>
    </td>
  </tr>
  <tr>
    <td>
      <b>License</b>
    </td>
    <td>
      <a href="https://github.com/BiomedicalMachineLearning/MultimodalCCI/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-BSD-blue.svg"
        alt="LICENSE"></a>
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**MMCCI** is a fast and lightweight Python package for integrating and visualizing CCI networks within and between multiple modalities at the level of the individual LR pair. It works on **scRNA-seq** and **spatial transcriptomics** data samples that have been processed through the following CCI algorithms:
1. stLearn
2. CellChat
3. CellPhoneDB
4. NATMI
5. Squidpy

## Getting Started

### Installation

MMCCI can be installed with `pip`

```
pip install multimodal-cci
```


### Documentation

Documentation and Tutorials are available here and we are commited to maintaining the software and addressing issues raised by users.

- There is a brain aging tutorial notebook [here](examples/brain_aging_example.ipynb)
- There is a melanoma tutorial notebook [here](examples/melanoma_example.ipynb)
- To understand how to load CCI results from different tools, look at this notebook [here](examples/loading_CCI_results.ipynb)

## CCI Integration

MMCCI allows users to integrate multiple CCI results together, both:
1. Samples from a single modality (eg. Visium)
2. Samples from multiple modalities (eg. Visium, Xenium and CosMX)

![Integration and Analysis Method](docs/images/analyses_pipeline.png)

## CCI Analysis

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

### Pipeline Diagram

![MMCCI Pipeline](docs/images/pipeline.png)

## Citing MMCCI

If you have used MMCCI in your research, please consider citing us: 
```
Hockey, L., Mulay, O., Xiong, Z., Khosrotehrani, K., Nefzger, C. M., & Nguyen, Q. (2024). MMCCI: Multimodal Cell-Cell Interaction Integrative Analysis of Single Cell and Spatial Data. bioRxiv. doi:10.1101/2024.02.28.582639
```




BSD License

Copyright (c) 2024, Genomics and Machine Learning lab
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
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