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

📥Download MetaX

abstract

Operational Taxon-Function (OTF)

Operational Taxon-Function (OTF) Unit: An operational unit which represents the association between specific taxa and biological functions.

OTF_Structure

OTF Analyzer

The Tools in OTF Analyzer

compostion

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 taxa and squares represent functions in the network.

Heatmap

Show all Taxa of a function.

Bar

Show all functions of a taxon

OTF Heatmap

Show OTFS intensity in groups(samples), e.g., Species-KO OTF Heatmap

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.

Download the MetaX Desktop Version

Lightweight annotation CLI
The default PyPI installation contains the OTF annotation backend and CLI without Qt:
```
python -m pip install MetaXTools
```
Run annotation with the same Python environment that installed MetaX:
```
python -m metax.cli.annotate --config annotation.yaml
```

Headless Analyzer and Report

Install the Analyzer without Qt, or install the complete headless Report stack:
python -m pip install "MetaXTools[analyzer]"
python -m pip install "MetaXTools[report]"
metax-report --config report.yaml

Desktop GUI / complete installation
The desktop profile includes Analyzer, statistics, plotting, Report, notebook export, and Qt:
```
python -m pip install "MetaXTools[full]"
metax
```
If an optional stack is missing, metax and metax-report exit with a clear message identifying the required extra.

Guidebook

Desktop Version(desktop):
- Refer to the MetaX Cookbook for detailed instructions on how to use MetaX with the graphical user interface.
Command-line version:
- See the Annotation CLI integration guide for global and unit-specific commands, configuration files, result JSON, exit codes, and subprocess integration.
- Read the example documentation in the Notebook for analysis examples.

Citing

If you use MetaX in your research, please cite the following publication:

Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics. Wu, Q., Ning, Z., Zhang, A., Zhang, X., Sun, Z., & Figeys, D. (2025). Analytical Chemistry. DOI: 10.1021/acs.analchem.4c06645.

Metadata

Release files for MetaXTools 2.6.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for MetaXTools 2.6.1
File	Size	Uploaded
metaxtools-2.6.1.tar.gz	8.8 MB	Jul 24, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for MetaXTools 2.6.1
File	Interpreter	ABI	Platform	Reset
metaxtools-2.6.1-py3-none-any.whl 8.9 MB Jul 24, 2026	Python 3	none	any	Details

Total release size: 17.7 MB

Release files / metaxtools-2.6.1.tar.gz

Download URL	metaxtools-2.6.1.tar.gz
Size	8.8 MB
Tags	Source
SHA-256 checksum How to use checksums	`3f6f4d64d8e592193ef99d7e65e8c2765b7e5c7d59733ec5c74e995c36ec24d1`
BLAKE2b-256 checksum How to use checksums	`b164532e87f3623e13e4f78a968ab5ca32dd9e7afeaca3eb51afe657064b1679`
Upload date	Jul 24, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.0.1 CPython/3.10.20`

Release files / metaxtools-2.6.1-py3-none-any.whl

Download URL	metaxtools-2.6.1-py3-none-any.whl
Size	8.9 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`e1310041184a077ea410a23f4ba7d34f74dff4cfdb86d5e7def1c745033a4dd6`
BLAKE2b-256 checksum How to use checksums	`7c505a11a0edfb823133e592e68dabe65b460d14e3c4ecb849ae5f76aa7890af`
Upload date	Jul 24, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.0.1 CPython/3.10.20`