byemaxx / MetaX

A novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics.

MetaX

MetaX is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics. We introduce the Operational Taxa-Functions (OTF) concept to explore microbial roles and interactions ("who is doing what and how") within ecosystems.

MetaX also features statistical modules and plotting tools for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.

Taxa-Functions Linkage

Linking Taxa and Functions in different levels of the hierarchy, and different functional categories. e.g., Species-KO, Genus-CAZy, Phylum-EC, etc.

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e.g. The KEGG Pathways linked to Roseburia hominis

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Download

Desktop Version(Recommended):

The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.

Download MetaX Desktop Version

Command-line version:

Clone the repository to your local machine and install the required dependencies.

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 MetaX Cookbook for detailed instructions on how to use MetaX wtih the graphical user interface.
  
  
• Command-line version:
  • Read the example documentation in the Notebook 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: 10.1101/2024.04.19.590315.