README.md

metadata

title: PhenoGenius
emoji: 🧞‍♂️
sdk: streamlit
sdk_version: 1.38.0
app_file: phenogenius_app.py
python_version: 3.11
pinned: true

PhenoGenius web app

Symptom interaction modeling for precision medicine

Overview

Symptom interaction model provide a method to standardize clinical descriptions and fully exploit phenotypic data in precision medicine.

This repository contains scripts and files to use PhenoGenius Web app, the phenotype matching system for genetic disease based on this model. Please try PhenoGenius in the cloud at https://huggingface.co/spaces/kyauy/PhenoGenius.

If you use PhenoGenius, please cite:

Yauy et al., Learning phenotypic patterns in genetic disease by symptom interaction modeling. medrXiv (2023). https://doi.org/10.1101/2022.07.29.22278181

Install

• Requirements

python == 3.11 #(pyenv install 3.11)
poetry #(https://python-poetry.org/docs/#installation)
git-lfs

• Install dependencies

poetry install

If you need to generate a requirements.txt file, use the following command:

poetry export --without-hashes --format=requirements.txt > requirements.txt

NB: if git-lfs is not installed, you won't be able to download PhenoGenius Web app resources.

Use streamlit webapp in your desktop

Run

poetry shell
streamlit run phenogenius_app.py

Enjoy !

Command line interface

The command line interface is available in the PhenoGenius client repository https://github.com/kyauy/PhenoGenius/.

License

PhenoGenius is licensed under the Apache License, Version 2.0. See LICENSE for the full license text.

Misc

PhenoGenius is a collaboration of :