ImageJ macro for the analysis of foci (e.g. DNA damage) in nuclei/cells

SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.

DNA Gap Prediction - using scikit-learn models to classify species and resolve gaps in DNA based on species.

X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction by Seale C and Gonçalves JP (Bioinformatics Advances 2025)

SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Seale C, and Gonçalves JP (bioRxiv 2024)

Research framework for POLE c.138del (p.Leu46Phefs*8) — an ultra-rare frameshift variant causing PPAP with ultra-hypermutated tumor phenotype (TMB >100 mut/Mb). Mechanistic models, therapeutic strategies, and experimental priorities.

MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis by Seale CF, Barazas M, van Schendel R, Tijsterman M, and Gonçalves JP (NAR Genomics and Bioinformatics 2025)

Predict mechanism underlying structural variants

HzHeal