[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

[![Build](https://github.com/theislab/ehrapy/actions/workflows/build.yml/badge.svg)](https://github.com/theislab/ehrapy/actions/workflows/build.yml)

[![Codecov](https://codecov.io/gh/theislab/ehrapy/branch/master/graph/badge.svg)](https://codecov.io/gh/theislab/ehrapy)

[![License](https://img.shields.io/github/license/theislab/ehrapy)](https://opensource.org/licenses/Apache2.0)

[![PyPI](https://img.shields.io/pypi/v/ehrapy.svg)](https://pypi.org/project/ehrapy/)

[![Python Version](https://img.shields.io/pypi/pyversions/ehrapy)](https://pypi.org/project/ehrapy)

[![Read the Docs](https://img.shields.io/readthedocs/ehrapy/latest.svg?label=Read%20the%20Docs)](https://ehrapy.readthedocs.io/)

[![Test](https://github.com/theislab/ehrapy/actions/workflows/test.yml/badge.svg)](https://github.com/theislab/ehrapy/actions/workflows/test.yml)

[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)

<img src="https://user-images.githubusercontent.com/21954664/156930990-0d668468-0cd9-496e-995a-96d2c2407cf5.png" alt="ehrapy logo">

# ehrapy overview

![fig1](https://github.com/user-attachments/assets/7927aa20-751c-4e73-8939-1e4b1c465570)

## Features

- Exploratory and targeted analysis of Electronic Health Records

- Quality control & preprocessing

- Visualization & Exploration

- Clustering & trajectory inference

## Installation

You can install _ehrapy_ via [pip] from [PyPI]:

```console

$ pip install ehrapy

```

## Usage

Please have a look at the [Usage documentation](https://ehrapy.readthedocs.io/en/latest/usage/usage.html) and the [tutorials](https://ehrapy.readthedocs.io/en/latest/tutorials/index.html).

```python

import ehrapy as ep

```

## Citation

[Heumos, L., Ehmele, P., Treis, T. et al. An open-source framework for end-to-end analysis of electronic health record data. Nat Med (2024). https://doi.org/10.1038/s41591-024-03214-0](https://www.nature.com/articles/s41591-024-03214-0).