Biostatistics Python Packages

crforest

Python toolkit for competing risks: forest (RSF) today; Fine-Gray + Aalen-Johansen + Gray's test + cause-specific Cox in v0.4. Scales to n=10⁶ in ~1 min, 10–22× faster than randomForestSRC on real EHR data, sklearn-compatible.

pyseqtarget

Estimation of the observational analogs of the intention-to-treat and per-protocol effects of hypothetical treatment strategies

comprisk

Python toolkit for competing risks: forest (RSF) today; Fine-Gray + Aalen-Johansen + Gray's test + cause-specific Cox in v0.4. Scales to n=10⁶ in ~1 min, 10–22× faster than randomForestSRC on real EHR data, sklearn-compatible.

pygna

A Python package for gene network analysis

survshap

SurvSHAP(t): Time-dependent explanations of machine learning survival models

biostatistics

An Intuitive App for Statistical Analysis

missingdata

missing data handing: visualize and impute

medicaid-utils

Python toolkit for Medicaid claims data analysis — preprocessing, cleaning, risk adjustment (Elixhauser, CDPS-Rx), quality measures (PQI, BETOS, low-value care), and patient-level analytic file construction for MAX and TAF CMS data. Built on Dask for scalable processing of large-scale healthcare claims datasets.

chai-one

An free and open source community implementation of Chai-1 in PyTorch

py4csr

Python for Clinical Study Reporting - Professional clinical trial reporting package

pmoss

Python package to model the p-value as an n-dependent function using Monte Carlo cross-validation.