Longitudinal Data Python Packages

scikit-longitudinal

Scikit-longitudinal is an open-source Python library for longitudinal data analysis, building on Scikit-learn's foundation with tools tailored for repeated measures data.

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.

echotime

EchoTime: explainable structural similarity for time series and time-series datasets, with shareable HTML reports and agent-ready JSON.

pyiomica

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

sctrial

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

multi-freq-ldpy

Multiple Frequency Estimation Under Local Differential Privacy in Python

latrend

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

sktime-dl

DEPRECATED, now in sktime - companion package for deep learning based on TensorFlow