Open-source tools for biomedical data science.

Scikit-learn compatible ComBat batch-effect correction.

Integrates Johnson, Fortin (neuroComBat), and Chen (CovBat) harmonization methods into scikit-learn pipelines, with leakage-safe cross-validation handling. Plugs into existing workflows without breaking the scikit-learn API contract.

pip install combatlearn

Nested cross-validation with calibration, threshold optimization, and statistical tests.

A toolkit for rigorous model evaluation: nested CV with hyperparameter selection kept inside the inner loop, probability calibration, decision-threshold tuning, and built-in statistical comparisons between models.

pip install nestkit

Automated Cas9 PAM-compatibility comparison with ClinVar integration.

A bioinformatic tool for comparing Cas9 nucleases across clinically relevant genomic contexts. Detects overlapping PAM sites between variants and identifies allele-specific targets arising from pathogenic mutations. Published in Frontiers in Genome Editing (2025).

APOBEC-style mutation identification from multiple sequence alignment.

Detects mutational patterns consistent with APOBEC enzyme activity from multiple sequence alignments, supporting downstream statistical description of mutational signatures.

Broken-stick model extension for metagenomic simulation.

Extends the CAMISIM metagenomic simulator with a broken-stick abundance model and a configurable number of strains, producing synthetic communities with controlled relative-abundance distributions for benchmarking metagenomic pipelines.

Interactive toolkit for sarcomeric morphometry and myofibril linearity analysis.

Combines image analysis with circular statistics and Monte Carlo simulations to quantify sarcomere geometry (aspect ratio, curviness, shape index) and myofibril alignment in skeletal-muscle micrographs.

pip install sarcostat