Awesome

Tests

</p> </div>

eds-scikit is a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data. It main goals are to:

Ease access and analysis of data
Allow a better transfer of knowledge between projects
Improve research reproducibility

Development

This library is developed and maintained by the core team of AP-HP’s Clinical Data Warehouse (EDS) with the strong support of Inria's SODA team.

How to use

Please check the online documentation for more informations. You will find

Detailed explanation of the project goal and working principles
A complete API documentation
Various Jupyter Notebooks describing how to use various functionnalities of eds-scikit
And more !

Requirements

eds-scikit stands on the shoulders of Spark 2.4 which requires:

Python ~3.7.1
Java 8

Installation

You can install eds-scikit via pip:

pip install "eds-scikit[aphp]"

:warning: If you get an an error during installation, please try downgrading pip via pip install -U "pip<23" before install eds-scikit`

:warning: If you don't work in AP-HP's ecosystem (EDS), please install via:

pip install eds-scikit

You can now import the library via

import eds_scikit

Contributing

You want to help on the project ?
You developped an interesting feature and you think it could benefit other by being integrated in the library ?
You found a bug ?
You have a question about the library ?
...

Please check our contributing guidelines.

Citation

If you use eds-scikit, please cite us as below.

@misc{eds-scikit,
    author = {Petit-Jean, Thomas and Remaki, Adam and Maladière, Vincent and Varoquaux, Gaël and Bey, Romain},
    doi = {10.5281/zenodo.7401549},
    title = {eds-scikit: data analysis on OMOP databases},
    url = {https://github.com/aphp/eds-scikit}
}

Acknowledgment

We would like to thank the following funders: