ODE modelling in Python
UK Health Security Agency (UKHSA)
Executive agency
https://www.gov.uk/government/organisations/uk-health-security-agency
Total FTE: 5,645·Digital & data FTE: 355
Stars of active repositories
129
Active repositories
94
Live repositories
204
Unavailable repositories
2
Languages of active repositories
- 1.Python (37%)
- 2.TypeScript (12%)
- 3.JavaScript (11%)
Active: currently on GitHub, not archived, and pushed to within 180 days. Live: currently on GitHub. Unavailable: previously on GitHub but not currently found.
GitHub accounts
ukhsa-collaboration, UKHSA-Internal, NHS-Test-Digital-Design (inactive)
Repositories
Showing all 94 active repositories, sorted by stars
Animal welfare assessment grid
Infrastructure for UKHSA data dashboard
Epidemiological Data Management
Front end for UKHSA data dashboard
UKHSA organisation standards
Public API and backend services for the UKHSA data dashboard
UKHSA API design guidelines.
Exploring how to quickly and easily design/prototype/deploy high quality digital forms for UK Gov. Based on the excellent work by DEFRA. Currently maintained by [email protected] at Caution Your Blast and a community collaboration between FCDO, HO, GDS, DfE, DIT, Version 1
Epidemiological Data Visualisation
One-function R package for adding a y-axis break symbol to a ggplot object
An application for NCBI taxonomy wrangling
This repository contains the R scripts, Stan scripts and Excel data sheets used in the publication "Robustly Quantifying Uncertainty in International Avian Influenza A(H5N1) Infection Fatality Ratios" by Gada et al. (2026).
Terraform module containing standard alarms
Nextflow process for running AMR detection using Abricate on ONT metagenomic samples
Repo containing Github Reusable Workflows. Repo managed by devops-github-repos
Backend for Find Public Health Resources.
Frontend for Find Public Health Resources.
UKHSA Cloud Engineering Standards
Template for standards documentation repositories
UKHSA Standards for Quality Assurance Testing
Development standards for engineering teams
Profiler: assign profiles to classified taxa. For use in the Orange Box.
A repository containing helper functions to interact with onyx analysis functionality.
UKHSA Ways of Working Standards
UKHSA development technology radar
Slurm Exporter is a Prometheus exporter designed to scrape and expose a comprehensive range of performance and scheduling metrics from Slurm-managed clusters. It supports both CPU and GPU resource accounting, node and partition state monitoring, job tracking, and scheduler statistics.
A script that generates a HTML report with synteny plots, given CLIMB IDs as input
ClasPar: the friendly classification parser that parses, filters and publishes analysis tables using various microbial classifier results. This tool is specifically developed for use in mSCAPE (Orange Box).
Template repository containing key files required for mSCAPE projects
Fork of PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data
Nextflow pipeline for characterisation of Streptococcus pneumoniae in metagenomic samples
External repository for sharing CDI logistic regression code
References for HCID check competitive mapping
Virus reclassification NextFlow pipeline
A Nextflow-based pipeline designed to process Nanopore-based data for GI bacterial characterisation.
Library stores tables for avian influenza mutations of concern.
Code for "Characteristics and factors associated with mortality of infants with Gram-negative bacteriemia in England, 2011-2019: A national retrospective cohort population-based surveillance data-linkage study"
Tool to gather and plot the negative control data and create summary HTML reports, and reports per site.
Negative Control summary reports and per site.
mSCAPE kubernetes orchestration module for downstream pathogen pipelines
UKHSA Terraform Modules to deliver a IaC self-service platform. Repo managed by devops-github-repos
A nextflow pipeline wrapping a tool that generates basic statistics given a fastq.gz as input
A nextflow pipeline wrapping geNomad
Exploiting network analysis to create a novel sentinel surveillance system for efficient, rapid detection of emerging Clostridioides difficile strains in England
A tool that generates basic statistics given a fastq.gz as input
Frontend component of the DevOps example project. Repo managed by devops-github-repos
Repo containing reusable Github Actions. Repo managed by devops-github-repos
A repository for the taxaplease container, which assigns taxa information.
Open sourcing code used in the Burden of Infectious Diseases Dashboard
Evaluation code for the PubHealthBench benchmark.
A fork of https://github.com/nhsuk/frontend-dotnetcore introducing some tweaks.
Container image used to run CI pipelines. Repo managed by devops-github-repos
Public mirror of the UKPID Backend application currently in development by Juicy Media.
This repository need to be created for integrating with APS which manage the creation of all orderable assets
OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages
Send POST request to trigger a webhook with GitHub Actions.