Clinical Data Python Packages

medpython

Medial Research Libs Infrastructure

pyhealth

A Deep Learning Python Toolkit for Healthcare Applications.

pycyclops

A toolkit for evaluating and monitoring AI models in clinical settings

omophub

Python SDK for OMOP/OHDSI vocabularies - query 11M+ medical concepts across SNOMED, ICD-10, RxNorm, LOINC & 120+ terminologies via simple API

ehrapy

Electronic Health Record Analysis with Python.

m4-infra

Give your AI agents clinical database access, research automation, and clinician-reviewed domain knowledge for MIMIC-IV, eICU, and more.

imperandi

CT/MR imaging preprocessing pipeline for DICOM harmonization, conversion, segmentation, radiomics & cohort building (medical imaging, Python CLI)

medpython-etl

Medial Research Tools for Machine learning in medical data, EMR

cleandat

Python functions to facilitate the pre-processing of data for ML tasks in a clinical context

yaib

🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

prevmed

Une plateforme minimaliste permettant aux utilisateurs non techniques de créer des questionnaires cliniques sans stocker de données personnelles. | A minimalist platform enabling non-technical users to create clinical questionnaires without storing personal data.

mosaic-harmonize

MOSAIC: Multi-site Optimal-transport Shift Alignment with Interval Calibration for clinical data harmonization

medkit-learn

The Medkit-Learn(ing) Environment: Medical Decision Modelling through Simulation (NeurIPS 2021) by Alex J. Chan, Ioana Bica, Alihan Huyuk, Daniel Jarrett, and Mihaela van der Schaar.