A curated list for preprocessing, cleaning, mapping and analyzing UK Biobank data.
- Tofu - Tofu is a Python tool for generating synthetic UK Biobank data.
- ukbschemas - Use R to generate a database containing the UK Biobank data schemas.
- Biobank Read - Python-based tools for the extraction, cleaning and pre-processing.
- FUNPACK - Python library for pre-processing of UK BioBank data.
- phemap - Python functions to map between ICD-10 terms and PheCodes.
- ukb_download_and_prep_template - Template for common processing operations.
- ukbiobank-loaders - a collection of Python tools to load data into Apache Parquet files developed by BenevolentAI.
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PHEASANT - Run a phenome scan pheWAS, Mendelian randomisation (MR)-pheWAS.
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ukbrest - Efficient and streamlined data access for reproducible research of large biobanks
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ukbb_parser - Python tool to extract datasets
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NETMAGE - NETMAGE: a humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS
- NealeLab GWAS statistics -- GWAS on latest UK Biobank data release using 4,203 phenotypes.
- Primary care EHR biomarkers -- machine-readable versions (CSV files) of electronic health record phenotyping algorithms for 31 commonly-measured biomakers.
- Docker utils - Docker image for UK Biobank utilities: ukbunpack, ukbfetch, ukblink, ukbgene, ukbmd5, ukbconv
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WikiMedMap mapping of phenotype strings from questionnaires in the UK Biobank and from Mendelian diseases in Online Mendelian Inheritance in Man (OMIM) database to eight vocabularies: International Classification of Diseases, Ninth Revision (ICD-9), ICD-10, ICD-O, Medical Subject Headings (MeSH), OMIM, Disease Database, and MedlinePlus.
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ukbb-srmed mapping of self-reported medication entries to the Anatomical Therapeutic Chemical (ATC) classification system and in the British National Formulary (BNF) coding systems.
Your contributions are always welcome!
Please submit a pull request or create an issue to add a new package, library or software to the list.
To the extent possible under law, Spiros Denaxas has waived all copyright and related or neighboring rights to this work.