# MetaX
**MetaX** is a novel tool for linking peptide sequences with taxonomic and functional information in **Metaproteomics**. We introduce the ***Operational Taxon-Function (OTF)*** concept to explore microbial roles and interactions ("**who is doing what and how**") within ecosystems.
MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.
## Operational Taxon-Function (OTF)
**Operational Taxon-Function (OTF) Unit**: An operational unit which represents the association between specific taxa and biological functions.
## OTFs Network
Linking Taxa and Functions in different levels of the hierarchy, and different functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc.
- 
e.g. The **KEGG Pathways** linked to ***Roseburia hominis***
- 
## Download
### `Desktop Version(Recommended)`:
The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.
<a href="https://shiny2.imetalab.ca/shiny/rstudio/metax_download/" target="_blank">Download MetaX Desktop Version</a>
<br>
### `Command-line version`:
Clone the repository to your local machine and install the required dependencies.
```bash
git clone https://github.com/byemaxx/MetaX.git
cd MetaX
python -m pip install -r requirements.txt
```
## Getting Started
- `Desktop Version(desktop)`:
- Refer to the <a href="https://byemaxx.github.io/MetaX/" target="_blank">MetaX Cookbook</a> for detailed instructions on how to use MetaX wtih the graphical user interface.
<br>
- `Command-line version`:
- Read the example documentation in the [Notebook](https://github.com/byemaxx/MetaX/blob/main/Docs/example.ipynb) for detailed instructions and examples.
## Citing MetaX
- If you use MetaX in your research, please cite the following publication:
- **MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF)**. *Wu, Q., Ning, Z., Zhang, A., Zhang, X., Sun, Z., & Figeys, D.* (2024). bioRxiv. DOI: <a href="https://doi.org/10.1101/2024.04.19.590315" target="_blank">10.1101/2024.04.19.590315</a>.
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