Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.

Extracting meaningful health information from large accelerometer datasets

Tofu is a Python tool for generating synthetic UK Biobank data.

Graph saliency maps through spectral convolutional networks for brain mapping

Sample code for ldsc analyses in UKBB

R functions for extracting diagnoses and first diagnosis dates from “Data-Field 41270” and “Data-Field 41280” in the UK Biobank, based on ICD-10 codes.

Python Software Development Kit (SDK) to process wearable sensor data

A tool for identifying patients in UK biobank given the definition of disease phenotypes (icd10, icd9, opcs or cancer histology).

Phenotyping algorithms for common biomarkers in primary care EHR for UK Biobank

snpnet - Efficient Lasso Solver for Large-scale genetic variant data

Python implementation of POPDx - Predictions for unseen, rare, and common labels.

Data management helper code for the UK Biobank.

Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

Aid researchers who work on the UKB RAP.

Preparatory scripts for BIDS tabular phenotypic data in large neuroimaging datasets.

Create binary traits for UKbio using ICD/OPER/medication/self reports/age of diagnosis/visit-dates etc). The current output includes variables on history, study visit, future, time-to-first-event, episode-duration. this is a starting point to construct your favorite trait in ukb. The code was written on the go, so not super clean code..

A PBWT-based light index for UK Biobank scale genotype data.

MultiVariate Polygenic Mixture Model

Identifying healthy individuals with Alzheimer neuroimaging phenotypes in the UK Biobank

Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort study

Rapid and accurate multi-phenotype imputation for millions of individuals

Code repository for paper: Fairness-Aware Data Augmentation for Cardiac MRI using Text-Conditioned Diffusion Models

Tools in Python to quickly start using the UK-BioBank dataset before UKB RAP.

UKB sleep Questionnaire Analysis 2025

Deep learning pipeline to obtain latent representation from images using 2D and 3D diffusion and other autoencoders

UK Biobank Tools

Command line tool written in c++ for easily extracting light and temperature data from Axivity AX3 accelerometers used in the UKBiobank

This is a custom UKB-MRI-Preprocessing pipeline. It can only run on the BIDS format and provides minimal QC.

Polygenic risk modeling with latent trait-related genetic components

Script for immunology and cognition analyses in UK Biobank