ukbiobank

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

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

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).

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..

MultiVariate Polygenic Mixture Model

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

Identifying healthy individuals with Alzheimer neuroimaging phenotypes in the UK Biobank

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