Extracting meaningful health information from large accelerometer datasets

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.

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

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

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

Python Software Development Kit (SDK) to process Axivity, GENEActiv, and Actigraph files

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

🫀 Code for "Neural network-based integration of polygenic and clinical information: Development and validation of a prediction model for 10 year risk of major adverse cardiac events in the UK Biobank cohort" 🫀

Data management helper code for the UK Biobank.

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

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

Tools for preprocessing, QC, and preliminary analyses from raw UK BioBank data

Aid Steno 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