Projects

Open-source code from my research.

UKBBGym
A population-scale benchmark for variant effect predictors. It scores predictors against phenotypes and plasma protein levels observed in carriers of ultra-rare variants in the UK Biobank.
Paper GitHub

ukbb-utils-gagneur
DNAnexus applets for preparing UK Biobank data on the Research Analysis Platform: phenotype and covariate extraction, genotype QC and variant annotation. Used for the UKBBGym analyses.
GitHub

FuncRVP
A Bayesian rare variant association framework that uses functional gene embeddings as a prior on gene effects, improving phenotype prediction and gene discovery.
Paper GitHub