Longitudinal Data Python Packages

scikit-longitudinal

Scikit-Longitudinal (Sklong) your tailored (health) Longitudinal machine learning library built on top of Scikit-Learn

pat2vec

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.

pyiomica

PyIOmica (pyiomica) is a Python package for omics analyses.

multi-freq-ldpy

Multiple Frequency Estimation Under Local Differential Privacy in Python

echotime

Explainable structural similarity for time series and time-series datasets.

sctrial

Participant-level differential analysis for longitudinal single-cell experiments: DiD, paired comparisons, module scoring, pseudobulk, and power analysis.

latrend

Python version similar to R latrend for longitudinal trajectory clustering and visualization.

sktime-dl

Deep learning extension package for sktime, a scikit-learn compatible toolbox for learning with time series data