semvec/pypi-packages huggingface dataset:
geneplexus 3.0.0
Network based gene classification
License: BSD 3-Clause License
Requires Python: >=3.10
Keywords: Network Biology, Supervised Learning, Gene Classification

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# PyGenePlexus [![DOI](https://zenodo.org/badge/423591778.svg)](https://zenodo.org/badge/latestdoi/423591778)

A Python package of the GenePlexus analysis pipeline.

* The [ModGenePlexus Method Paper](https://www.biorxiv.org/content/10.1101/2025.08.11.669721v1.abstract)
* The [GenePlexusZoo Method Paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011773)
* The [GenePlexus Benchmarking Paper](https://academic.oup.com/bioinformatics/article/36/11/3457/5780279)
* The [Webserver](https://www.geneplexus.net/)
* The [Package Documentation](https://pygeneplexus.readthedocs.io)
* Data [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14750555.svg)](https://doi.org/10.5281/zenodo.14750555)

# Quick start

## Installation

Install the ``GenePlexus`` package via ``pip``.

```bash
pip install geneplexus
```

## Run GenePlexus pipline

### Example script

See `example/example_run.py` for example usage of the API.

For other examples see [Package Documentation](https://pygeneplexus.readthedocs.io).

### Command-line interface

```bash
geneplexus --input_file example/input_genes.txt --output_dir example_result
```

Run ``geneplexus --help`` to see full CLI options.

# Dev

## Installation

Install the PyGenePlexus package in editable mode with dev dependencies

```bash
pip install -e ."[dev]"
```

## Testing

Run the default test suite

```bash
pytest test/
```

By default, test data will be cached. Thus, after the first test run, data redownload will not be tested. To force redownload, specify the ``--cache-clear`` option

```bash
pytest test/ --cache-clear
```

## Building Documentation

1. Install doc dependencies

```bash
pip install -r docs/requirements.txt
```

2. Build

```bash
cd docs
make html
```

3. Open doc

```bash
open build/html/index.html
```