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https://github.com/s-bell/awesome-uk-biobank

A curated list of UK Biobank related resources
https://github.com/s-bell/awesome-uk-biobank
List: awesome-uk-biobank
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A curated list of UK Biobank related resources
Host: GitHub
URL: https://github.com/s-bell/awesome-uk-biobank
Owner: s-bell
Created: 2022-06-01T09:51:45.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2023-07-06T10:28:17.000Z (over 1 year ago)
Last Synced: 2024-04-22T01:00:31.048Z (8 months ago)
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Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
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README

        # UK Biobank resources



    


    A curated list of UK Biobank related resources



    

    



    

    



## Contents

- [Official quicklinks](#official-quicklinks)

- [Phenomewide association studies](#phenomewide-association-studies)

- [Derivation of variables](#derivation-of-variables)

    - [Questionnaire](#questionnaire)

    - [Electronic health records](#electronic-health-records)

    - [Clinical and biochemical](#clinical-and-biochemical)

    - [Accelerometer](#accelerometer)

- [Genetics](#genetics)

- [Imaging](#imaging)

    - [Brain](#brain-mri)

    - [Cardiac](#cardiac-mri)

    - [Abdominal](#abdominal-mri)

    - [Optical coherence tomography and fundus](#optical-coherence-tomography-and-fundus)

- [Data processing](#data-processing)

- [Misc](#misc)

- [Contributing](#contributing)

## Official quicklinks

- [Researcher login](https://bbams.ndph.ox.ac.uk/ams/)

- [Data showcase](https://biobank.ndph.ox.ac.uk/showcase/)

- [DNAnexus Research Analysis Platform](https://ukbiobank.dnanexus.com/login/) (RAP)

- [Twitter feed](https://twitter.com/uk_biobank)

- [Genomics mailing list](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=UKB-GENETICS)

- [Neuroimaging mailing list](https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A0=UKB-NEUROIMAGING)

## GWAS summary data / other resources

- [Neale lab (4,203 phenotypes)](https://www.nealelab.is/uk-biobank)

- [PanUK Biobank (7,228 phenotypes)](https://pan.ukbb.broadinstitute.org/)

- [GeneAtlas (778 phenotypes)](http://geneatlas.roslin.ed.ac.uk)

- [Global Biobank Engine (~3,800 phenotypes)](https://biobankengine.stanford.edu/)

- [UK Biobank TOPMed-imputed PheWeb (1,419 phenotypes)](https://pheweb.org/UKB-TOPMed/)

- [Lee lab (~1,400 phenotypes)](https://www.leelabsg.org/resources)

- [MRC IEU (2,514 phenotypes)](https://gwas.mrcieu.ac.uk/datasets/?gwas_id__icontains=ukb-b)

- [Genebass (4,529 phenotypes)](https://app.genebass.org)

- [AstraZeneca PheWAS portal (~15,500 binary and ~1,500 continuous phenotypes)](https://azphewas.com/)

- [Oxford Brain Imaging Genetics Server (~4,000 phenotypes)](https://open.win.ox.ac.uk/ukbiobank/big40/)

- [UNC School of Medicine GWAS summary statistics for brain imaging Phenotypes](https://www.med.unc.edu/bigs2/data/gwas-summary-statistics/)

- [Sex-stratified GWAS of 530 phenotypes](https://datashare.ed.ac.uk/handle/10283/3908)

- [ExPheWas browser (1,746 phenotypes)](https://exphewas.statgen.org/)

- [GWAS summary statistics for 82 heart imaging traits](https://zenodo.org/record/5606168)

- [Gene-based tests for 1,403 phecodes and 827 continuous phenotypes](https://zenodo.org/record/4477703)

- [Rivas lab (35 blood and urine biomarkers)](https://github.com/rivas-lab/biomarkers)

- [Nightingale Health NMR measures and their ratios in ~115,000 participants](https://gwas.mrcieu.ac.uk/datasets/?gwas_id__icontains=met-d)

- [Mitochondrial PheWas](https://zenodo.org/record/4609973)

- [29 blood cell traits](https://t.ly/Nnga)

- [Telomere length](https://figshare.com/s/caa99dc0f76d62990195)

- [10 resting-state brain networks](https://zenodo.org/record/7034803)

- [Nonsuicidal self-injury (NSSI)](https://github.com/WashU-BG/nssi_gwas)

Many of these, and more, are available via the fantastic [MRC IEU OpenGWAS](https://gwas.mrcieu.ac.uk/datasets/) project.

## Perform phenome-wide association studies

| Tool | Description|

|------|------------|

| [PHESANT](https://github.com/MRCIEU/PHESANT) | PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc) in UK Biobank |

| [createUKBphenome](https://github.com/umich-cphds/createUKBphenome) | Create a PheWAS code based phenome using ICD9 and ICD10 data from baskets of the UK Biobank |

## Derivation of variables

### Questionnaire

| Tool | Description|

|------|------------|

| [ukbb-srmed](https://github.com/PhilAppleby/ukbb-srmed) | Match terms in the UK Biobank self-reported medication data coding table with terms in both the Anatomical Therapeutic Chemical (ATC) classification system and in the British National Formulary (BNF) |

| [ukbfrailty](https://github.com/dylwil/ukbfrailty) | Stata code to generate a frailty index based on 49 items in UK Biobank |

| [ukbiobank_lca_model_predictions](https://github.com/dcmuller/ukbiobank_lca_model_predictions) | Stata programs to calculate risk of lung cancer based on a UK Biobank prediction model |

### Electronic health records

| Tool | Description|

|------|------------|

| [ukb-biomarker-phenotypes](https://github.com/spiros/ukb-biomarker-phenotypes) | Phenotyping algorithms for 31 commonly-measured biomakers in primary care   electronic health records |

| [ukbb-ehr-data](https://github.com/philipdarke/ukbb-ehr-data) | Clean and prepare UK Biobank primary care electronic health records for research |

| [ukbbhelpr](https://github.com/philipdarke/ukbbhelpr) | A collection of helper functions primarily for working with linked primary care electronic health record data in UK Biobank |

| [phemap](https://github.com/spiros/phemap) | Functions to map between ICD-10 terms and PheCodes for UK Biobank hospital electronic health records |

| [UKBCaseFinder](https://github.com/yeyixuan/UKBCaseFinder) | A tool for identifying patients in UK Biobank given the definition of disease phenotypes (ICD-10, ICD-9, OPCS or cancer histology) |

| [ukbcodes](https://github.com/SurgicalInformatics/ukbcodes) | Returns suggestions of equivalent codes based on UK Biobank mappings |

| [UKB.COVID19](https://github.com/bahlolab/UKB.COVID19) | UK Biobank COVID-19 data processing and risk factor association tests |

### Clinical and biochemical

| Tool | Description |

|---|---|

| [ukbnmr](https://github.com/sritchie73/ukbnmr) | Tools for processing Nightingale NMR biomarker data in UK Biobank |

| [CAHDbyECG](https://github.com/andywxf/Predict_CAHD_by_ECG_on_UK_Biobank) | Predict coronary atherosclerotic heart disease from electrocardiogram |

| [NeuralCVD](https://github.com/thbuerg/NeuralCVD) | Contains code to preprocess UK Biobank data and train the NeuralCVD score (neural network-based integration of polygenic and clinical information of a prediction model for 10 year risk of major adverse cardiac events) |

| [UKB_bioage](https://github.com/jonathanklmak/UKB_bioage_cancer) | Clinical biomarker-based biological ageing in the UK Biobank |

### Accelerometer

| Tool | Description |

|------|-------------|

| [biobankAccelerometerAnalysis](https://github.com/OxWearables/biobankAccelerometerAnalysis) | A tool to extract meaningful health information from large accelerometer datasets |

| [BiobankActivityCSF](https://github.com/CASSON-LAB/BiobankActivityCSF) | Process the accelerometer CWA files from the UK Biobank activity monitoring study in Python |

| [snake-ukb-accel](https://github.com/tgbrooks/ukbb) | Snakemake pipeline to process and aggregate the actigraphy data in the UK Biobank |

| [axivity-ax3-tool](https://github.com/jlc-christie/axivity-ax3-tool) | Command line tool for easily extracting light and temperature data from Axivity AX3 accelerometers used in the UK Biobank |

| [UKBiobankKineticEnergyHarvesting](https://github.com/CASSON-LAB/UKBiobankKineticEnergyHarvesting) | Software for processing the UK Biobank accelerometer datasets in the paper 'Estimation of kinetic energy harvesting potential for self-powered wearable devices' | 

| [ssl-wearables](https://github.com/OxWearables/ssl-wearables) | Self-supervised learning for wearables using the UK-Biobank (>700,000 person-days) |

## Genetics

| Tool | Description|

|------|------------|

| [MoChA](https://github.com/freeseek/mocha) | MOsaic CHromosomal Alterations (MoChA) caller |

| [MT_UKB](https://github.com/GrassmannLab/MT_UKB) | Compute mtDNA abundance estimates |

| [mt_PheWAS](https://github.com/clody23/UKBiobank_mtPheWas/) | Custom scripts used for mtSNVs variant recalling in UK Biobank |

| [ddpop](https://github.com/marcustuke/ddpop) | Detect large DNA duplications/deletions in UK Biobank Affymetrix Axiom array data |

| [cnv-ukb](https://github.com/priestlab/cnv-ukb) | Contains scripts used to call CNVs using UK Biobank data |

| [ukbb-pytorch-dataloader](https://github.com/hrushikeshloya/ukbb-pytorch-dataloader) | Load genotype data from UK Biobank into PyTorch |

| [go-bgen](https://github.com/carbocation/bgen) | BGEN file format reader for parsing UK Biobank and other genotype data in Go |

| [liftover_plink_beds](https://github.com/dnanexus-rnd/liftover_plink_beds) | Converting UK Biobank genome-wide genotyping data from one reference build to another |

| [ukb-phasing](https://github.com/browning-lab/ukb-phasing) | A pipeline for phasing 200,031 sequenced genomes in the UK Biobank on RAP |

| [μ-PBWT](https://github.com/dlcgold/muPBWT) | A PBWT-based light index enabling storage and use of UK Biobank scale genotype data on a commodity laptop |

| [DNANexus_GRS](https://github.com/hdg204/DNANexus_GRS) | An R Function for calculating genetic risk scores in the UK Biobank cohort using DNA Nexus |

## Imaging phenotypes

### Brain MRI

| Tool | Description |

|------|-------------|

| [ukb-brain-imaging](https://www.fmrib.ox.ac.uk/ukbiobank/fbp) | UK Biobank brain imaging processing pipeline |

| [tvb-ukbb](https://github.com/McIntosh-Lab/tvb-ukbb) | TheVirtualBrain implementation of the UK Biobank imaging pipeline |

| [qsm-pipeline](https://git.fmrib.ox.ac.uk/cwang/uk_biobank_qsm_pipeline) | MATLAB scripts for QSM processing of the UK Biobank swMRI data |

| [XTRACT_atlases](https://github.com/SPMIC-UoN/XTRACT_atlases) | Extract 42 white matter tract atlases |

| [ukbiobank-spinalcord-csa](https://github.com/sct-pipeline/ukbiobank-spinalcord-csa) | Analysis pipeline to normalise spinal cord cross-sectional area |

| [brain-age](https://github.com/ha-ha-ha-han/UKBiobank_deep_pretrain) | Pretrained neural networks for brain age prediction in UK Biobank from MRI images |

| [slice2vol](https://github.com/alexbagur/slice2vol) | Slice-to-Volume Registration for UK Biobank data |

| [brain-sex](https://github.com/LeoBman/brain-sex-classification) | Predict participant sex from brain MRI images |

| [PSMD](http://www.psmd-marker.com/) | PSMD is a robust, fully-automated and easy-to-implement marker for cerebral small vessel disease based on diffusion tensor imaging, white matter tract skeletonization (as implemented in FSL-TBSS) and histogram analysis |

| [ePVS quantification](https://hub.docker.com/r/giorgioberardini/pvs5) | Docker image to quantify enlarged perivascular spaces (n.b. [preprocessing](https://hub.docker.com/r/giorgioberardini/pvs_preproc) should be performed first) |

| [morpho-deepsulci](https://github.com/brainvisa/morpho-deepsulci) | Deep learning methods for Morphologist sulci recognition |

| [ENIGMA-SULCI](https://hub.docker.com/r/fpizzaga/sulci) | Docker image for the sulci protocol from the ENIGMA-SULCI working group that combines Freesurfer and BrainVISA to robuslty segment and label 123 sulci across the whole brain |

| [adni_phenotypes](https://github.com/tjiagoM/adni_phenotypes) | Identifying healthy individuals with Alzheimer neuroimaging phenotypes in the UK Biobank |

| [generative_brain_controlnet](https://github.com/Warvito/generative_brain_controlnet) | Train ControlNet on FLAIR images in UK Biobank using MONAI Generative Models |

### Cardiac MRI

| Tool | Description |

|------|-------------|

| [ukbb_cardiac](https://github.com/baiwenjia/ukbb_cardiac) | A toolbox used for processing and analysing cardiovascular magnetic resonance (CMR) images |

| [ukbb_lax_4ch](https://github.com/priestlab/ukbb_lax_4ch_segmentation) | Segmenting and measuring long-axis 4-chamber view cardiac MRI data sets |

| [CardioRadiomics](https://github.com/iremcetin/radiomics_cardio_risk_factors) | Radiomics signatures of cardiovascular risk factors from cardiac MRI |

| [ukb-cardiac-mri](https://github.com/HazyResearch/ukb-cardiac-mri) | Weakly supervised classification of aortic valve malformations using unlabeled cardiac MRI sequences |

| [cardiac-fractals](https://zenodo.org/record/3698268) | Artificial intelligence derived fractal structure of the heart |

### Abdominal MRI

| Tool | Description |

|------|-------------|

| [ReCOH_pipeline](https://github.com/recoh/pipeline) | Image processing and quality control for abdominal MRI in the UK Biobank |

| [ukbb-mri-sseg](https://github.com/calico/ukbb-mri-sseg/) | Semantic segmentation for Dixon abdominal MRI and other modalities by Calico |

| [ukb-kidney-segmentation](https://github.com/tarolangner/ukb_segmentation) | Kidney morphology |https://github.com/alexbagur/pancreas-segmentation-ukbb |

| [UKBiobankDXAMRIPreprocessing](https://github.com/rwindsor1/UKBiobankDXAMRIPreprocessing) | Code for downloading and preprocessing (and stitching) MRI and DXA data from the UK Biobank | 

| [AAC_scoring](https://github.com/calico/AAC_scoring) | Map DEXA images from UK Biobank dataset to abdominal aortic calcification scores  |

| [ukb_mimir](https://github.com/tarolangner/ukb_mimir) | An inference engine for UK Biobank neck-to-knee MRI |

| [ukb_segmentation](https://github.com/tarolangner/ukb_segmentation) | PyTorch implementation for 2.5D U-Net segmentation of UK Biobank neck-to-knee body MRI |

| [iliopsoas_muscle](https://github.com/recoh/iliopsoas_muscle) | Large-scale analysis of iliopsoas muscle volumes in the UK Biobank |

| [PDFF](https://github.com/marcsous/pdff) | Proton density fat fraction calculation for MRI |

| [UKBB-GNC-Abdominal-Segmentation](https://github.com/BioMedIA/UKBB-GNC-Abdominal-Segmentation) | Python pipeline for automated imaging-based abdominal organ segmentation in UK Biobank |

### Optical coherence tomography and fundus

| Tool | Description |

|------|-------------|

| [OCT-Converter](https://github.com/marksgraham/OCT-Converter) | Tools for extracting the raw optical coherence tomography and fundus data from proprietary file formats |

| [VAMPIRE](https://vampire.computing.dundee.ac.uk/) | VAMPIRE (Vessel Assessment and Measurement Platform for Images of the REtina) is a software application for efficient, semi-automatic quantification of retinal vessel properties with large collections of fundus camera images |

| [Retina-Seg](https://github.com/vineet1992/Retina-Seg) | Automatically segment vasculature from retinal fundus photographs |

## Data processing

| Tool | Description |

|------|-------------|

| [UKB_RAP](https://github.com/dnanexus/UKB_RAP) | Access share reviewed code & Jupyter Notebooks for use on the UK Biobank Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops |

| [ukbtools](https://github.com/kenhanscombe/ukbtools) | An R package to manipulate and explore UK Biobank data |

| [ukbwranglr](https://github.com/rmgpanw/ukbwranglr) | An R package for UK Biobank data wrangling |

| [ukbwranglrextra](https://github.com/rmgpanw/ukbwranglrextra) | Extra add-on functions for ukbwranglr |

| [ukbwranglr_resources](https://github.com/rmgpanw/ukbwranglr_resources) | A collection of resources to support ukbwranglr |

| [ukbREST](https://github.com/hakyimlab/ukbrest) | Efficient and streamlined data access for reproducible research of large biobanks |

| [ukbcc](https://github.com/tool-bin/ukbcc) | Tool for curation of UK Biobank data to generate cohorts |

| [ukbm](https://github.com/neurodatascience/ukbm) | Code for management of UK Biobank bulk data |

| [bulk-ukb](https://github.com/adigherman/UKB) | Download UK Biobank bulk data  |

| [UKBioPick](https://github.com/CirculatoryHealth/UKBioPick) | Extract fields of interest from a UK Biobank tab-delimited phenotypic file (ukbxxxx.tab) |

| [BiobankRead-Bash](https://github.com/saphir746/BiobankRead-Bash) | Python scripts to extract and pre-process UK Biobank data |

| [precimed-ukb](https://github.com/precimed/ukb) | Helper tools to process UK Biobank data |

| [UKBFetchbash](https://github.com/GordonMatthewson/UKBFetchbash) | Bash script to download your application's approved bulk data files from the UK Biobank dataset |

| [ukbb-slicer](https://github.com/webhash/ukbb-slicer) | Slice large UK Biobank CSV files in a memory efficient way |

| [R-ukbiobank](https://github.com/adamleejohnson/R-ukbiobank) | Contains a collection of functions that facilitate the extraction of phenotypes from UK Biobank data |

| [ukbb_parser](https://github.com/nadavbra/ukbb_parser) | A Python module for loading phenotypic and genetic data from the UK Biobank |

| [ukb_download_and_prep_template](https://github.com/OxWearables/ukb_download_and_prep_template) | Facilitates common data pre-processing steps when working with UK Biobank data |

| [UKBiobank-Table-Conversion](https://github.com/futurologist/UKBiobank-Table-Conversion) | Conversion of data tables extracted from UK Biobank into new regression-friendly data tables  |

| [ukbpheno](https://github.com/niekverw/ukbpheno) | An R package for efficiently munging the files provided by UK Biobank to generate data tables of with unified format for further analysis |

| [ukb_healthoutcomes_db](https://github.com/ccbs-stradl/ukb_healthoutcomes_db) | Store and work with UK Biobank record-level health outcomes in a SQLite database |

| [UKBWeightsFinal](https://github.com/sjoerdvanalten/UKBWeightsFinal) | Derive weights for UK Biobank to address selection bias using the 2011 Census |

| [ukb-rap-tools](https://github.com/pjgreer/ukb-rap-tools) | Scripts and workflows for use analysing UK Biobank data from the DNANexus Research Analysis Platform |

| [UKBBcleanR](https://github.com/machiela-lab/UKBBcleanR) | Prepare electronic medical record data from the UK Biobank for time-to-event analyses |

| [ukbiobank-loaders](https://github.com/BenevolentAI/ukbiobank-loaders) | Convert UK Biobank electronic health data into Apache Parquet files that are easier to read, and a library that provides different methods to access the data |

| [Rdna-nexus](https://github.com/hdg204/Rdna-nexus) | Functions to analyse UK Biobank genetic data directly from DNA Nexus' RStudio Workbench |

## Misc

| Tool | Description |

|------|-------------|

| [UK-Biobank-scraper](https://github.com/lwaw/UK-Biobank-scraper) | A script that will download meta-data from the UK Biobank website and return a json object |

| [UKBscrape](https://github.com/asoroosh/UKBscrape) | Scrapes the UK Biobank website to provide a built-in dictionary for the field IDs. Also checks which variables are not included in your application compared to the website |

| [ukbschemas](https://github.com/bjcairns/ukbschemas) | Use R to generate a database containing the UK Biobank data [schemas](http://biobank.ctsu.ox.ac.uk/crystal/schema.cgi) |

| [docker-ukbiobank-utils](https://github.com/spiros/docker-ukbiobank-utils) | Docker versions of the utilities provided by UK Biobank |

| [tofu](https://github.com/spiros/tofu) | Tofu is a Python library for generating synthetic UK Biobank data |

| [BBS](https://github.com/choishingwan/BBS) | Simulation software for generating phenotypes from UK Biobank data |

## Contributing

Please submit a pull request or create an issue to add a new resource to the list - software, packages, tutorials or similar welcomed. 

[Return to top](#uk-biobank-resources)