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HDRUK / Repo explorer

All 198 public alphagov repositories, filterable and sortable.

All 198 public repositories. Commits, authors and file counts come from the mirrored git history; type and team come from the GOV.UK Developer Documentation where it covers the repository. Type to filter; click a column heading to sort.

Repository Language Git size Commits Authors Files Type Team Status
papers
Extract of publications that mention HDR-UK
Python4.4 GB4,022952active CI bot
datasets
HDR UK Gateway Datasets
Python3.7 GB1,6221452active CI
manuscript_code
Manuscript code for our paper: bit.ly/bloodcellgwas
R628.3 MB15513,164active
mvcm-api
Python384.3 MB257213,457active CI docker
synthea
Synthetic Patient Population Simulator
Java309.8 MB5,3621401,552active CI
gatk
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see t
Java263.3 MB14,5481531,427active
openpathology-web
Openpathology website
Jupyter Notebook181.3 MB16891,798active
EPACTS
C++181.0 MB1067518active
RDMP
Research Data Management Platform (RDMP) is an open source application for the loading,linking,a
C#157.2 MB9,479344,676active CI bot
ringbp
R136.6 MB19333active docker
covid19_asymptomatic_trans
R129.1 MB92419active
openprescribing
A Django app providing a REST API and dashboards for the HSCIC's GP prescribing data
Python127.9 MB7,04035958active CI bot docker
HDRUK_AppliedML
This repository contains code and supporting material for the HDRUK Summer School Course on Appl
Python112.2 MB4158active
software_differences_paper
Jupyter Notebook109.2 MB27673active
data-profiles
Sample Gateway Data Profiles
Python97.8 MB7119active
hie-training
HDR UK Health Information Engineering Module
Jupyter Notebook91.5 MB3276active
Biomarker_Identification
Biomarker Identification for Bravo, Williams, Gkoutos and Acharjee
-90.3 MB4211active
researchfish-data-analysis
HTML76.0 MB1365133active
ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
Perl71.3 MB1,97932465active docker
synthea-profiling
HTML69.9 MB236135active
clinical-trials
Python67.9 MB651128active CI
comix_covid-19-first_wave
Code and data from the analysis of the 1st wave of the CoMix 2020 contacts survey
R60.8 MB10445active
ldsc
LD Score Regression (LDSC)
Python59.1 MB576251,093active
HDR-UK_Webmapping_in_R
How to use leaflet to make an interactive map using child obesity at reception year data in Engl
HTML58.6 MB16112active
treeseq-inference
Work for the tree sequence inference paper.
Python58.3 MB1,629891active
safepeopleregistry-web
NextJS Frontend component for Safe People Registry
TypeScript57.9 MB5,067271,809active CI docker
bedtools2
bedtools - the swiss army knife for genome arithmetic
C49.9 MB2,1591121,085active CI
gateway-web-old
HDR UK Gateway Web
JavaScript44.9 MB7,129711,376archived CI docker
BRASS
Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.
Perl39.4 MB45811115active docker
cohort-discovery-service-web
Cohort Discovery Service (Web)
TypeScript37.9 MB2,18418754active CI docker
cgpBattenberg
Battenberg algorithm and associated implementation script
Perl32.0 MB3371628active docker
drug_target_lof
Evaluating potential drug targets through human loss-of-function genetic variation
R28.0 MB24298active
clustering_w2v
Python27.4 MB7245active
predCAN
Ontology-based prediction of cancer driver genes
Python27.0 MB12215active
gateway-web
TypeScript26.7 MB7,642391,794active CI docker
covid-mobility-tracker
Generate maps from google mobility data
-23.8 MB20218active
safepeopleregistry-api
Laravel API making up the Safe People Registry backend component
PHP23.1 MB3,98326914active CI docker
data-use-register
In the repo, all the scrapped data from Data Access Links will be uploaded individually.
-21.0 MB30321active
Data-Science-for-Docs
Data Science For Practicing Clinicians
HTML20.3 MB66568336active
synthea-international
Synthea metadata and configuration files for international locations
Python19.8 MB6912313active
covid19_cases_from_deaths
Shiny app to infer caes from new deaths of COVID-19
R18.4 MB841031active
gateway-api
gateway api 2.0
PHP18.3 MB9,216401,740active CI docker
data-utility-tools
HTML18.1 MB3258active
hilton-keeling-estimating-R0
The code in this repository accompanies our upcoming paper "Estimation of country-level basic re
HTML17.3 MB12138active
fma-dataloads
FMA ingestion script
Python15.5 MB2501125active docker
EHRtemporalVariability
HTML14.6 MB43440active
clockwork
CRyPTIC data processing pipelines
HTML14.3 MB34415890active CI docker
schemata-old
HDR UK Schemas
HTML13.6 MB36317741archived CI
CaRROT-Docs
Documentation
HTML13.5 MB4541710active CI
tpot
A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic
Python13.3 MB2,461135151active CI
accredited-researchers-api
Accredited Researchers API Stub
JavaScript12.3 MB2355,237active docker
MedCATweb
This repo provides a simple interface to inspect, improve and add concepts to biomedical NER+L m
Python12.3 MB1,30021285active CI bot docker
covid-uk
Scenario analyses for COVID-19 outbreak in the United Kingdom
R11.7 MB26435active
MetaXcan
MetaXcan software and manuscript
Python10.8 MB58727318active
search-service
Go9.5 MB4552739active CI docker
cohort-discovery-service-nlp
NLP Service for Cohort Discovery Service
Python9.5 MB3001462active CI docker
uvR
R package to support analysing UVR data
R9.2 MB34218active
somop
synthetic omop generator
Python8.1 MB20342active
GatewayAutomation
Regression Automation test scripts
-8.0 MB531active
phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
Java7.0 MB208629active docker
gateway-api-old
HDR UK Gateway API
JavaScript6.4 MB3,79772459archived CI bot docker
hutch
Former repo for Hutch
C#6.3 MB2,884211archived
phenotype-library
HDR UK National Phenotype Library
SCSS6.2 MB243111,712active
hackathon-entity-linkage
HTML5.5 MB69762active docker
phenotypes
HDR UK National Phenotype Library
SCSS5.2 MB13871,361archived
CPRD_HES_variability
R5.1 MB5234active
Gateway-Frontend
Health Data Gateway Frontend - react App
CSS5.0 MB57515181active docker
react-core
HTML4.6 MB1344230active
DWGSIM
Whole Genome Simulator for Next-Generation Sequencing
C4.5 MB1671241active
cohort-discovery-service-docs
HTML4.4 MB97560active CI
PGS_Catalog
An open database of polygenic scores and relevant metadata needed to apply and evaluate them cor
Python4.3 MB1,21810283active CI
collaborathon-2020-team3
HDR UK Collaborathon Team3 Submission
-4.1 MB1015active
DaCVaP
R3.8 MB651096active
schemata
Jupyter Notebook3.6 MB66025342active CI
Winterfell
Generate complex, validated and extendable JSON-based forms in React.
JavaScript3.5 MB4853235active
common-api
OpenAPI definitions for the Federated Data Sharing Common API
-3.2 MB84114active
uprn-match
M3.0 MB3938332active
CaRROT-Pseudonymisation
Jupyter Notebook2.8 MB21333active CI
KGPhenotyping
knowledge graph based phenotyping
Java2.4 MB67541active
hdruk-phd-handbook
Handbook for the HDRUK-Turing PhD Programme in Health Data Science
CSS2.3 MB210866active
COVID19_clustersize
Analysis of COVID-19 transmission using cluster size distribution
HTML2.2 MB25216active
cCFRDiamondPrincess
HTML2.1 MB19230active
cohort-discovery-service-api
PHP2.0 MB1,44716408active CI docker
tools
HDR UK Gateway Tools
Python1.9 MB1,13947active CI
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
C1.8 MB1,0745080active CI
CaRROT-CDM
Python1.7 MB1,16719102active CI
Gateway-Auth-Server
JavaScript1.7 MB2022417active docker
loftee
Perl1.7 MB1601567active
los_review
Code used to produce the results presented in "A rapid review of evidence for hospital length of
TeX1.7 MB52723active
Gateway-Middleware
Health Data Gateway - GraphQL Apollo Middleware
JavaScript1.6 MB2811946archived docker
risk-score-builder
Map clinical risk score concepts to structured definitions using ontologies, calculate structure
Python1.6 MB14548active
MedCAT
Medical Concept Annotation Tool
Python1.5 MB1,5184082active docker
2019nCoV_proportion_asym
R1.5 MB39422active
ScienceCOPEMethodsCode
Code accompanying map generation in Drew et al. Science manuscript
Jupyter Notebook1.5 MB213active
traser
JavaScript1.5 MB4482062active CI docker
gateway-api-csharp-sdk
C#1.4 MB51868active
uk-postcode-mapper
Python1.3 MB12126active docker
gateway-api-java-sdk
Java1.3 MB31862active
hdruk_summerschool_session_1_2
Docker image for first two sessions at the HDRUK summer school 2019
Jupyter Notebook1.2 MB16210active docker
medicines-dashboard
A medicine dashboard
JavaScript1.1 MB127550active CI docker
web-application-tutorial-recorder
Record browser journeys, add narration, and export polished tutorial videos — all from a local w
JavaScript1.1 MB29225active
py-carrot-mapper
Jupyter Notebook1.0 MB9219active
gateway-2-integrations-testing
Jupyter Notebook957.4 kB621228active CI
gateway-api-python-sdk
Python956.4 kB51849active
sythentic-covid19-dataset
HTML809.0 kB12238active
gateway-api-go-sdk
Shell804.9 kB31602active
gateway-widgets
Gateway widgets for collaborators
JavaScript757.8 kB6679active
hdruk-ui
Shared components library
TypeScript738.3 kB118868active CI
covid-19
HDR UK - Resources for 🦠COVID-19 Research
-655.4 kB8751active
gateway-metadata-integrations
Go650.2 kB2451735active CI docker
safepeopleregistry-api-csharp-sdk
C#580.6 kB21310active
safepeopleregistry-api-java-sdk
Java570.4 kB21305active
safepeopleregistry-api-go-sdk
Go541.7 kB21197active
bhpm
Bayesian Hierarchical Possion Models for Mulitple Grouped Outcomes with Clustering
R513.0 kB142285active
OpenID-Connect-PHP
Minimalist OpenID Connect client
PHP508.9 kB60112115active CI bot
chronological-map-phenotypes
Machine-readable version of electronic health record phenotypes for Kuan V. and Denaxas S. et al
-500.7 kB787588active
rake-nltk
Python implementation of the Rapid Automatic Keyword Extraction algorithm using NLTK.
Python499.7 kB103983active CI
dpclust
Dirichlet Process based methods for subclonal reconstruction of tumours
R480.3 kB404872active docker
vec2sparql
SPARQL Endpoint with functions for computing embedding similarities
Java478.2 kB61546active docker
RF-FeatureSelection-PowerAnalysis
R468.0 kB2114active
20190927_IntroductionGithub_HDRUK
-452.6 kB3515active
ADR-graph
Predicting adverse drug reactions from a knowledge graph
Python429.1 kB23121active
discovery-api
Discovery API
HTML427.0 kB424active CI
gateway-api-typescript-sdk
TypeScript427.0 kB31286active
nextjs-messenger
TypeScript407.6 kB26485active CI
safepeopleregistry-api-python-sdk
Python402.4 kB21292active
traser-mapping-files
Python377.9 kB4461860active CI
mongodb-data-analysis-visualisation
Jupyter Notebook374.8 kB9211active
4C-Initiative
4C-Initiative
R371.7 kB1112active
treeSeg
Implementation of the treeSeg algorithm as an R package.
Jupyter Notebook323.6 kB23541active
ontologies
-313.3 kB1215active
screening_outbreak_delay
R310.3 kB11110active
oss
HDR UK OSS Contributions
Python306.2 kB1477188active CI
PGM
MATLAB284.7 kB4237active
CPRD_UTI_sepsis_elderly
This is the R code and code lists used to analyse the data for paper "Antibiotic prescribing for
R269.3 kB20224active
metadata-visualiser
helper function and maps for visualising metadata transformations
Jupyter Notebook264.2 kB9214active
gateway-api-rust-sdk
Rust257.0 kB31561active
UK-OMOP
A directory of OMOP data sets in the UK
Jupyter Notebook249.9 kB32210active
term-extraction-director
Term extraction director service (TED)
Python222.2 kB2141932active CI docker
reference-codes
General reference codes
Python217.1 kB339active CI
cardio
Pulse oximetry data processing and classification
Python199.7 kB91518active
medcat-service
JavaScript196.6 kB145818active CI docker
seqtk
Toolkit for processing sequences in FASTA/Q formats
C187.4 kB13498active
MedCATservice
Running MedCAT as a RESTful web service
Python185.3 kB2491443active CI bot docker
safepeopleregistry-api-rust-sdk
Rust174.1 kB21190active
fma-custodian-test-server
A test BE server for federated metadata automation
TypeScript142.3 kB1131045active CI docker
safepeopleregistry-api-typescript-sdk
TypeScript140.3 kB21101active
spr-signed-payload-generator-examples
This repository provides example implementations for generating signed payloads required to auth
C++130.0 kB8110active
github-actions-templates
Centralized GitHub Actions workflows and reusable pipelines for CI/CD automation
-113.7 kB154313active CI
gateway-helm-charts
A collection of helm charts based on applications
Smarty107.5 kB4138active
gateway-outbound
gateway outbound
TypeScript101.4 kB147726active docker
uk-vaccine-breakthrough-autumn-2022
R98.3 kB6246active
gateway-workflow
HDR UK Gateway Workflow
Java96.3 kB85845active docker
OMOP
Community for OMOP users in the UK
-79.9 kB79211active
dar-integration-sandbox
Test server for DAR outbound integration
Go76.8 kB51218active docker
simple-gcp-logging
JavaScript71.7 kB2757active
mvGWAMA
Python script for multivariate GWAS meta-analysis
Python59.4 kB2243active
hackathon-projects-2025
Project code for Hackathon 2025.
-58.4 kB26113active
.github
HDR UK Github Profile
-52.2 kB914active
laravel-gdpr-tools
PHP50.2 kB3233active CI
laravel-messenger
PHP48.1 kB9123active CI
gw-api-widget
gateway api widget
TypeScript44.0 kB37525active docker
FM-summary
Fine-mapping method only using summary statistics
R37.9 kB213active
hdruk-feature-configurations
This is where the configuration file lives for the features enabled in the gateway.
-34.8 kB6445active CI
laravel-mjml
A Laravel extension to make use of MJML API
PHP34.8 kB56914active
lrTaps
Shell30.7 kB24112active
treeImbalance
An R package for detecting asymmetry in time-sampled phylogenetic trees.
R29.7 kB21231active
Electronic-Monitoring-Device-Adherence-Typology
Study Aim: To construct a data-driven multi-dimensional typology of medication non-adherence in
R28.7 kB1015active
Gateway-DB
Health Data Gateway - PostgreSQL Database
PLpgSQL28.7 kB31720active
multiomic_AITD
Scripts associated with the paper doi: https://doi.org/10.1101/662957
R27.6 kB229active
HDRUK-fellows-day-2018
Machine Learning Resources collected from the HDRUK UK Fellows's day 2018 (2018-11-15)
-22.5 kB835active
hdr_uk_demo
HDR UK Summer School demo for Image Registration
Jupyter Notebook22.5 kB713active
glossary
HDR UK Glossary and Acronyms
-20.5 kB322active
artificialMHR
Python19.5 kB514active
laravel-hubspot-manager
HubSpot integration manager
PHP19.5 kB5224active CI
TRE-Survey
HTML17.4 kB814active
gateway-web-components
Web Components for HDRUK
JavaScript17.4 kB1926active
accessibility-statement
-16.4 kB521active
laravel-plugin-core
Provides a core modular Plugin system to apply to Laravel API projects
PHP16.4 kB11211active
ESCs_models
Agent-based modelling of pattern formation in embryonic stem cells
NetLogo14.3 kB313active
claims-based-access-control
A claims based access control package for Laravel 12.x.
PHP14.3 kB17410active
gw-spatial-filter
gateway spatial filter
TypeScript12.3 kB4226active docker
laravel-model-states
PHP12.3 kB12212active
resource_manager
This is a simple resource manager
Python11.3 kB1243active
laravel-search-and-filter
A simple package for adding search and sorting capabilities to your eloquent models.
PHP10.2 kB1245active
vascular-ageing
Container for Python analysis codes regarding "Prediction of vascular ageing based on smartphone
Python10.2 kB424active
demo
HTML9.2 kB1633active
laravel-job-failed-slack-notification
Automatically sends detailed Slack notifications whenever a Laravel queued job fails, including
PHP8.2 kB817active
PhenomicsLibrary
-6.1 kB331active
mongodb-sync
Script to sync mongodb databases
JavaScript6.1 kB427active docker
GBMD
-5.1 kB112active
jokes-app-test
JavaScript5.1 kB114active
hdruk_bbmri_hack
Python4.1 kB1023active
rquest-omop-worker-workflows
Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/
Common Workflow Language4.1 kB446active
hdruk
-2.0 kB312active CI
COALESCE
-1.0 kB523active
hdruk-repo-template
A template for base HDR UK Repositories
-1.0 kB112active
hdruk_summerschool_session1
EHR analysis for the HDR UK summer school 2019
Dockerfile1.0 kB223active docker