eds-scikit is a Python library providing tools to
Project description
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:
Project details
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