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    150 repositories

    • tools

      Public
      HDR UK Gateway Tools
      Python
      •0•0•0•1•Updated Oct 10, 2024Oct 10, 2024

    • papers

      Public
      Extract of publications that mention HDR-UK
      publicationshdruk2019-ncovcoronaviruscovid-19sars-cov
      Python
      •
      MIT License
      •4•8•2•37•Updated Oct 10, 2024Oct 10, 2024

    • traser-mapping-files

      Public
      Python
      •0•0•0•1•Updated Oct 9, 2024Oct 9, 2024

    • schemata-2

      Public
      Jupyter Notebook
      •0•1•0•3•Updated Oct 9, 2024Oct 9, 2024

    • 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
      •33•0•0•11•Updated Oct 6, 2024Oct 6, 2024

    • 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 Oct 4, 2024Oct 4, 2024

    • OpenID-Connect-PHP

      Public
      Minimalist OpenID Connect client
      PHP
      •
      Apache License 2.0
      •363•0•0•1•Updated Sep 28, 2024Sep 28, 2024

    • gateway-api

      Public
      HDR UK Gateway API
      hdrukhdruk-gateway
      JavaScript
      •
      Apache License 2.0
      •2•6•0•28•Updated Sep 13, 2024Sep 13, 2024

    • synthea

      Public
      Synthetic Patient Population Simulator
      Java
      •
      Apache License 2.0
      •644•1•0•0•Updated Sep 7, 2024Sep 7, 2024

    • uprn-match

      Public
      M
      •
      Apache License 2.0
      •2•0•0•31•Updated Sep 4, 2024Sep 4, 2024

    • gateway-web

      Public
      HDR UK Gateway Web
      hdrukhdruk-gateway
      JavaScript
      •
      Apache License 2.0
      •5•9•0•16•Updated Aug 30, 2024Aug 30, 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
      •2•7•11•5•Updated Aug 19, 2024Aug 19, 2024

    • MedCAT

      Public
      Medical Concept Annotation Tool
      hdruk
      Python
      •
      Apache License 2.0
      •102•0•0•2•Updated Aug 12, 2024Aug 12, 2024

    • seqtk

      Public
      Toolkit for processing sequences in FASTA/Q formats
      C
      •
      MIT License
      •308•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • DaCVaP

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

    • MedCATservice

      Public
      Running MedCAT as a RESTful web service
      Python
      •14•0•0•3•Updated Jul 30, 2024Jul 30, 2024

    • tpot

      Public
      A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
      Python
      •
      GNU Lesser General Public License v3.0
      •1.6k•0•0•1•Updated Jul 25, 2024Jul 25, 2024

    • clockwork

      Public
      CRyPTIC data processing pipelines
      HTML
      •
      MIT License
      •22•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • ontologies

      Public
      1•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • datasets

      Public
      HDR UK Gateway Datasets
      hdrukdatasets
      Python
      •
      Apache License 2.0
      •7•24•0•18•Updated Jul 16, 2024Jul 16, 2024

    • dpclust

      Public
      Dirichlet Process based methods for subclonal reconstruction of tumours
      R
      •
      GNU Affero General Public License v3.0
      •16•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • chronological-map-phenotypes

      Public
      Machine-readable version of electronic health record phenotypes for Kuan V. and Denaxas S. et al.
      publicationsphenotypeshdruk
      MIT License
      •40•0•0•2•Updated Jun 28, 2024Jun 28, 2024

    • fma-custodian-test-server

      Public
      A test BE server for federated metadata automation
      TypeScript
      •0•0•0•0•Updated Jun 20, 2024Jun 20, 2024

    • predCAN

      Public
      Ontology-based prediction of cancer driver genes
      hdruk
      Python
      •
      BSD 2-Clause "Simplified" License
      •4•0•0•2•Updated Jun 17, 2024Jun 17, 2024

    • laravel-mjml

      Public
      A Laravel extension to make use of MJML API
      PHP
      •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • UK-OMOP

      Public
      A directory of OMOP data sets in the UK
      Jupyter Notebook
      •0•1•0•0•Updated May 21, 2024May 21, 2024

    • EHRtemporalVariability

      Public
      HTML
      •
      Apache License 2.0
      •8•2•0•0•Updated May 4, 2024May 4, 2024

    • openpathology-web

      Public
      Openpathology website
      better-carehdrukhdruk-better-carehdruk-science
      Jupyter Notebook
      •
      MIT License
      •1•1•0•10•Updated May 1, 2024May 1, 2024

    • bwa

      Public
      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
      C
      •
      GNU General Public License v3.0
      •556•0•0•0•Updated Apr 16, 2024Apr 16, 2024