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Summary:
A comprehensive Python package for healthcare data engineering, designed to extract, transform, and feature engineer patient data from CogStack-based electronic health record (EHR) datalakes. It provides tools for cohort building, batch data processing, clinical note analysis, and creating machine learning-ready datasets.
Latest version:
0.3.1
Required dependencies:
accelerate
|
colorama
|
eland
|
elasticsearch
|
faker
|
fuzzywuzzy
|
huggingface-hub
|
ipykernel
|
medcat
|
numpy
|
pandas
|
paramiko
|
peft
|
polars
|
psycopg2-binary
|
python-pptx
|
rapidfuzz
|
scikit-learn
|
seaborn
|
sqlalchemy
|
torch
|
transformers
Optional dependencies:
bokeh
|
dask
|
datasets
|
jupyterlab
|
lifelines
|
matplotlib-venn
|
myst-parser
|
nbconvert
|
nbformat
|
nbmake
|
nbstripout
|
nltk
|
numba
|
openpyxl
|
pre-commit
|
pydot
|
pyodbc
|
pytest
|
python-tds
|
sphinx
|
sphinx-autodoc-typehints
|
sphinx-rtd-theme
|
sphinxcontrib-mermaid
|
statsmodels
|
umls-api
|
wordcloud
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