UK Public Sector Code by Organisation

ODE modelling in Python

Animal welfare assessment grid

Infrastructure for UKHSA data dashboard

UKHSA organisation standards

Epidemiological Data Management

Front end for UKHSA data dashboard

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

UKHSA Conference Website 2023

UKHSA Standards for Quality Assurance Testing

Template for standards documentation repositories

UKHSA development technology radar

UKHSA Cloud Engineering Standards

UKHSA Ways of Working Standards

testing the use of git-repo-filter

Profiler: assign profiles to classified taxa. For use in the Orange Box.

Development standards for engineering teams

Pipeline to analyse clinical metagenomic samples

Nextflow pipeline for characterisation of Streptococcus pneumoniae in metagenomic samples

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).

A repository containing helper functions to interact with onyx analysis functionality.

Nextflow workflow for mSCAPE sample processing through the Orange Box.

A script that generates a HTML report with synteny plots, given CLIMB IDs as input

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.

Template repository containing key files required for mSCAPE projects

Fork of PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data

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"

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 geNomad

Frontend component of the DevOps example project. Repo managed by devops-github-repos

Repo containing reusable Github Actions. Repo managed by devops-github-repos

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.

OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages

Send POST request to trigger a webhook with GitHub Actions.