Longitudinal Data Python Packages

haenv

HAEnv — synthetic longitudinal patients with code-derived gold, for evaluating health agents over time

scikit-longitudinal

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

pygformula

The pygformula implements the parametric g-formula in Python. The parametric g-formula (Robins, 1986) uses longitudinal data with time-varying treatments and confounders to estimate the risk or mean of an outcome under hypothetical treatment strategies specified by the user.

gp3sequencespy

Transparent, reproducible sequence analysis in Python. Audit ordered categorical data, discover recurring structure, compare trajectories, model transitions and latent states, test group differences, and report every analytical choice.

pyiomica

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

paneldx

Validate longitudinal dataset as what it claims to be. Entity-key verification, leakage detection, cumulative-counter traps and naive baselines, as a library, a CLI and a CI gate.

neurotcs

Public portfolio for NeuroTCS, a citation-locked longitudinal medical AI audit framework.

multi-freq-ldpy

Multiple Frequency Estimation Under Local Differential Privacy in Python

pat2vec

A comprehensive Python package for healthcare data engineering, designed to extract, transform, and feature engineer patient data from CogStack-based EHR datalakes. Enables patient-level aggregation, longitudinal time series construction (up to 25 years retrospective), flexiblefeature engineering (biochemistry, demographics, medications, diagnoses

echotime

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

sctrial

Trial-Aware Statistical Inference for Single-Cell Data

sktime-dl

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

latrend

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