Explainable Machine Learning in Survival Analysis

Open source bioinformatics and computational biology toolbox written in F#. This is the core package containing type models and parsers/writers.

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

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

Biostatistics resources : reading list, RMarkdown notebooks, and more!

Toolbox for biostatistics and clinical data analysis in R. Developed by the biostatistics team at Laboratorios Sophia S.A. de C.V.

📗handbook of biostatistic and R

🎯 📕 Targeted Learning in R: A Causal Data Science Handbook

Group sequential design for clinical trials

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

Conquering confounds and covariates: methods, library and guidance

SAS code snippets

R package for High dimensional data analysis and integration with O2PLS!

R package for fitting joint models to time-to-event data and multivariate longitudinal data

Clinical Trial Simulations

A Python package for gene network analysis

Analysis of simulation studies including Monte Carlo error

Claude Code skills for medical research — literature search, reporting guidelines, statistical analysis, publication figures. Built by a physician-researcher, tested on real publications. MIT licensed.

Power and Sample Size Calculation

Repository that contains all the data, code and manuscript files for a paper that explores the use of GAMs in biomedical research.