# 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.
## OTF Analyzer
The Tools in OTF Analyzer
## OTF Examples
Linking Taxa and Functions in different levels of the hierarchy, and various functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc. Lots of visualization tools can be selected.
**Network**
**Dots** represent <u>taxa</u> and **squares** represent <u>functions</u> in the network.
- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net.png" alt="OTF" style="zoom: 50%;" />
**Heatmap**
Show all Taxa of a function.
- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_heatmap.png" alt="tf_link_heatmap" style="zoom:50%;" />
**Bar**
Show all functions of a taxon
- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_bar.png" alt="tf_link_bar" style="zoom:50%;" />
**OTF Heatmap**
Show OTFS intensity in groups(samples), e.g., **Species-KO** OTF Heatmap
<img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/otf_heatmap.png" alt="otf_heatmap" style="zoom:50%;" />
## Download & Installation
- **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 the MetaX Desktop Version</a>
<br>
- **Command-line version**
> Use [PyPi](https://pypi.org/project/MetaXTools/) to install, then type `metax` in the terminal to launch the GUI.
>
> `python -m pip install MetaXTools`
## Guidebook
- `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 with 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
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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"description": "# MetaX\r\n\r\n**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. \r\n\r\nMetaX also features <u>statistical modules</u> and <u>plotting tools</u> for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.\r\n\r\n\r\n\r\n\r\n## Operational Taxon-Function (OTF)\r\n\r\n**Operational Taxon-Function (OTF) Unit**: An operational unit which represents the association between specific taxa and biological functions. \r\n\r\n\r\n\r\n## OTF Analyzer\r\n\r\nThe Tools in OTF Analyzer\r\n\r\n\r\n\r\n## OTF Examples\r\n\r\nLinking Taxa and Functions in different levels of the hierarchy, and various functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc. Lots of visualization tools can be selected.\r\n\r\n**Network**\r\n\r\n**Dots** represent <u>taxa</u> and **squares** represent <u>functions</u> in the network.\r\n\r\n- <img src=\"https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net.png\" alt=\"OTF\" style=\"zoom: 50%;\" />\r\n\r\n\r\n\r\n**Heatmap**\r\n\r\nShow all Taxa of a function.\r\n\r\n- <img src=\"https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_heatmap.png\" alt=\"tf_link_heatmap\" style=\"zoom:50%;\" />\r\n\r\n**Bar**\r\n\r\nShow all functions of a taxon\r\n\r\n- <img src=\"https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_bar.png\" alt=\"tf_link_bar\" style=\"zoom:50%;\" />\r\n\r\n**OTF Heatmap**\r\n\r\nShow OTFS intensity in groups(samples), e.g., **Species-KO** OTF Heatmap\r\n\r\n<img src=\"https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/otf_heatmap.png\" alt=\"otf_heatmap\" style=\"zoom:50%;\" />\r\n\r\n## Download & Installation\r\n- **Desktop Version** (Recommended)\r\n\r\n > The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.\r\n >\r\n > <a href=\"https://shiny2.imetalab.ca/shiny/rstudio/metax_download/\" target=\"_blank\">Download the MetaX Desktop Version</a>\r\n\r\n<br>\r\n\r\n- **Command-line version**\r\n\r\n > Use [PyPi](https://pypi.org/project/MetaXTools/) to install, then type `metax` in the terminal to launch the GUI.\r\n >\r\n > `python -m pip install MetaXTools`\r\n\r\n\r\n\r\n## Guidebook\r\n\r\n- `Desktop Version(desktop)`:\r\n - Refer to the <a href=\"https://byemaxx.github.io/MetaX/\" target=\"_blank\">MetaX Cookbook</a> for detailed instructions on how to use MetaX with the graphical user interface.\r\n <br>\r\n- `Command-line version`:\r\n - Read the example documentation in the [Notebook](https://github.com/byemaxx/MetaX/blob/main/Docs/example.ipynb) for detailed instructions and examples.\r\n\r\n\r\n## Citing\r\nIf you use MetaX in your research, please cite the following publication:\r\n\r\n> **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>.\r\n\r\n",
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