Research software

Open tools for interpretable biology.

Software developed alongside my research for extracting biological signal from complex single-cell and epigenomic data.

ALPINE package icon

ALPINE

A semi-supervised NMF framework that separates phenotype- and batch-associated signals from shared biological variation in multicondition single-cell RNA-seq data.

Single-cell RNA-seqPhenotype decodingInterpretable NMFBatch correction
Python · BSD-3-Clause
Genome Research · 2025
MONTE package icon

MONTE

A cancer label-free framework for estimating tumor purity and recovering tumor-intrinsic, CpG-resolved profiles from bulk DNA methylation data.

DNA methylationTumor purityMethylation correctionTransfer learning
Python · BSD-3-Clause
bioRxiv preprint · 2026