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Biostatistics Python Packages

Python packages with the GitHub topic biostatistics. Sorted by relevance, with stars and monthly downloads.
sunnyadn
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.

2K 4 0
CausalInference
pyseqtarget

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

2K 2 0
sunnyadn
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.

1K 4 0
stracquadaniolab
pygna

A Python package for gene network analysis

937 33 6
MI2DataLab
survshap

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

818 97 16
hikarimusic
biostatistics

An Intuitive App for Statistical Analysis

450 8 3
raamana
missingdata

missing data handing: visualize and impute

269 18 1
uc-cms
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.

266 9 3
kyegomez
chai-one

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

182 3 0
yanmingyu92
py4csr

Python for Clinical Study Reporting - Professional clinical trial reporting package

133 0 0
BIIG-UC3M
pmoss

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

78 16 5
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