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    153 repositories

    • papers

      Public
      Extract of publications that mention HDR-UK
      publicationshdruk2019-ncovcoronaviruscovid-19sars-covgit-scraping
      Python
      •
      MIT License
      •4•10•2•10•Updated Apr 1, 2025Apr 1, 2025

    • MetaXcan

      Public
      MetaXcan software and manuscript
      Python
      •
      Other
      •94•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • PGS_Catalog

      Public
      An open database of polygenic scores and relevant metadata needed to apply and evaluate them correctly.
      Python
      •
      Apache License 2.0
      •5•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • MedCATweb

      Public
      This repo provides a simple interface to inspect, improve and add concepts to biomedical NER+L model (e.g. MedCAT) and a further interface for research specific training data collection
      hdruk
      Python
      •
      Other
      •35•0•0•11•Updated Mar 24, 2025Mar 24, 2025

    • bwa

      Public
      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
      C
      •
      GNU General Public License v3.0
      •555•0•0•0•Updated Mar 22, 2025Mar 22, 2025

    • schemata

      Public
      enhanced-gateway
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•4•Updated Mar 20, 2025Mar 20, 2025

    • traser-mapping-files

      Public
      enhanced-gateway
      Python
      •0•0•0•4•Updated Mar 19, 2025Mar 19, 2025

    • gateway-api-old

      Public archive
      HDR UK Gateway API
      hdrukhdruk-gateway
      JavaScript
      •
      Apache License 2.0
      •3•6•0•33•Updated Mar 14, 2025Mar 14, 2025

    • laravel-mjml

      Public
      A Laravel extension to make use of MJML API
      PHP
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • bedtools2

      Public
      bedtools - the swiss army knife for genome arithmetic
      C
      •
      MIT License
      •292•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • datasets

      Public
      HDR UK Gateway Datasets
      datasetshdrukgit-scraping
      Python
      •
      Apache License 2.0
      •7•26•0•13•Updated Mar 9, 2025Mar 9, 2025

    • uprn-match

      Public
      M
      •
      Apache License 2.0
      •3•1•0•31•Updated Mar 7, 2025Mar 7, 2025

    • oss

      Public
      HDR UK OSS Contributions
      ossgithub-starsgatewayhdr-uk
      Python
      •
      MIT License
      •6•23•5•2•Updated Mar 6, 2025Mar 6, 2025

    • hackathon-entity-linkage

      Public
      HTML
      •0•0•0•2•Updated Mar 5, 2025Mar 5, 2025

    • OpenID-Connect-PHP

      Public
      Minimalist OpenID Connect client
      PHP
      •
      Apache License 2.0
      •382•0•0•1•Updated Mar 4, 2025Mar 4, 2025

    • MedCATservice

      Public
      Running MedCAT as a RESTful web service
      Python
      •14•0•0•2•Updated Feb 26, 2025Feb 26, 2025

    • UK-OMOP

      Public
      A directory of OMOP data sets in the UK
      Jupyter Notebook
      •1•1•0•0•Updated Feb 25, 2025Feb 25, 2025

    • fma-custodian-test-server

      Public
      A test BE server for federated metadata automation
      TypeScript
      •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • gateway-2-integrations-testing

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • tools

      Public
      HDR UK Gateway Tools
      Python
      •0•0•0•1•Updated Jan 14, 2025Jan 14, 2025

    • mvGWAMA

      Public
      Python script for multivariate GWAS meta-analysis
      Python
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Dec 6, 2024Dec 6, 2024

    • synthea

      Public
      Synthetic Patient Population Simulator
      Java
      •
      Apache License 2.0
      •715•1•0•0•Updated Nov 17, 2024Nov 17, 2024

    • gateway-web-old

      Public archive
      HDR UK Gateway Web
      hdrukhdruk-gateway
      JavaScript
      •
      Apache License 2.0
      •5•9•0•16•Updated Nov 6, 2024Nov 6, 2024

    • hackathon-projects-2025

      Public
      Project code for Hackathon 2025.
      3•6•0•0•Updated Nov 1, 2024Nov 1, 2024

    • synthea-international

      Public
      Synthea metadata and configuration files for international locations
      Python
      •
      Apache License 2.0
      •36•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • RDMP

      Public
      Research Data Management Platform (RDMP) is an open source application for the loading,linking,anonymisation and extraction of datasets stored in relational databases.
      C#
      •
      GNU General Public License v3.0
      •16•0•0•16•Updated Aug 21, 2024Aug 21, 2024

    • CaRROT-CDM

      Public
      Python
      •
      MIT License
      •1•7•11•4•Updated Aug 19, 2024Aug 19, 2024

    • MedCAT

      Public
      Medical Concept Annotation Tool
      hdruk
      Python
      •
      Apache License 2.0
      •105•1•0•2•Updated Aug 12, 2024Aug 12, 2024

    • seqtk

      Public
      Toolkit for processing sequences in FASTA/Q formats
      C
      •
      MIT License
      •310•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • DaCVaP

      Public
      R
      •
      Creative Commons Attribution 4.0 International
      •2•2•0•1•Updated Aug 1, 2024Aug 1, 2024