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.

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); Confirmed germline pathogenic frameshift variant clinically consistent w/ PPAP (reported ultra-hypermutated; tumour signature confirmation pending). Mechanistic models, differential diagnosis, therapeutic strategies, and experimental priorities.

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

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)

Ancient DNA repair framework

HzHeal

Predict mechanism underlying structural variants