UK Public Sector GitHub Observatory
All 153 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 |
|---|---|---|---|---|---|---|---|---|
| kmerid | C | 500.0 MB | 17 | 3 | 155 | active | ||
| data_management_system | Ruby | 473.9 MB | 2,556 | 28 | 3,150 | active CI bot | ||
| snapperdb | Python | 376.5 MB | 243 | 16 | 30 | active | ||
| PneumoCaT Pneumococcal Capsular Typing tool for NGS data | Python | 340.9 MB | 129 | 6 | 86 | active | ||
| gemmm | Python | 207.3 MB | 55 | 4 | 50 | active CI | ||
| snapperdb_references | - | 158.5 MB | 4 | 1 | 269 | active | ||
| coimeail A Nextflow-based pipeline designed to process Nanopore-based data for GI bacterial characterisat | Python | 123.5 MB | 1 | 1 | 82 | active | ||
| covid19-app-system-public COVID19 app backend | Kotlin | 101.3 MB | 61 | 13 | 1,433 | archived docker | ||
| snp-search | Ruby | 100.3 MB | 85 | 3 | 33 | active | ||
| fingertips-open | C# | 79.8 MB | 64 | 6 | 3,207 | active | ||
| foodscanner_compute | PHP | 70.7 MB | 67 | 9 | 80 | active docker | ||
| ukhsa-science-research-site-dev | HTML | 69.1 MB | 3,143 | 19 | 307 | active CI | ||
| LOMA A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads. | Nextflow | 62.9 MB | 243 | 6 | 363 | active | ||
| ntbs_Beta | C# | 56.8 MB | 5,964 | 44 | 1,028 | active CI bot docker | ||
| pygom ODE modelling in Python | Jupyter Notebook | 49.6 MB | 834 | 31 | 197 | active CI | ||
| COVID-19-app-iOS-BETA Source code of the Beta of the NHS COVID-19 iOS app | Objective-C | 46.1 MB | 3,068 | 37 | 361 | archived CI | ||
| foodscanner_swaps_api | PHP | 43.2 MB | 64 | 5 | 101 | active docker | ||
| covid-19-app-ios-ag-public COVID19 iOS App | Swift | 42.7 MB | 52 | 1 | 2,033 | archived | ||
| SOMA A Nextflow pipeline designed to classify, align and assemble short-read metagenomic sequencing | Nextflow | 35.7 MB | 110 | 2 | 387 | active | ||
| github-pages-deploy-action | TypeScript | 34.5 MB | 1,342 | 38 | 54 | active CI bot docker | ||
| gpha-mscape-hcid-refs References for HCID check competitive mapping | Python | 34.0 MB | 8 | 3 | 6 | active CI | ||
| UKHSA_Immensa_analysis | R | 33.5 MB | 22 | 8 | 30 | active | ||
| ukhsa-science-research-site | HTML | 33.3 MB | 280 | 13 | 285 | active CI | ||
| PneumoKITy Fork of PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data | Python | 30.1 MB | 243 | 14 | 46 | active CI docker | ||
| drivers_epidemic_dynamics_from_nhs_covid19_app Code for the publication "Drivers of epidemic dynamics in real time from daily digital COVID-19 | R | 28.5 MB | 2 | 2 | 66 | active | ||
| core-access | Ruby | 26.4 MB | 39 | 6 | 64 | active | ||
| digital-form-builder Exploring how to quickly and easily design/prototype/deploy high quality digital forms for UK Go | TypeScript | 25.9 MB | 4,292 | 134 | 1,048 | active CI bot docker | ||
| r-lib-actions | JavaScript | 23.6 MB | 1,029 | 140 | 26,735 | active CI | ||
| gpha-mscape-nf-amr Nextflow process for running AMR detection using Abricate on ONT metagenomic samples | Python | 22.6 MB | 1,182 | 5 | 41 | active CI | ||
| epiviz Epidemiological Data Visualisation | R | 13.1 MB | 432 | 9 | 258 | active CI | ||
| science-research-site Research at PHE | CSS | 12.9 MB | 60 | 6 | 227 | active CI | ||
| slurm_exporter Slurm Exporter is a Prometheus exporter designed to scrape and expose a comprehensive range of p | Go | 12.5 MB | 383 | 30 | 181 | active CI docker | ||
| mind-your-ps-2021-manuscript-code | Python | 12.1 MB | 10 | 4 | 27 | active | ||
| ntbs-reporting | TSQL | 11.7 MB | 1,130 | 32 | 337 | active CI | ||
| MOST | Python | 11.7 MB | 31 | 6 | 102 | active | ||
| covid-19-app-android-ag-public COVID19 Android app | Kotlin | 11.6 MB | 62 | 8 | 1,980 | archived | ||
| gpha-tb-intreeactive intreeactive is a tool to create a single, portable interactive phylogeny using Python and a han | HTML | 11.1 MB | 35 | 2 | 41 | active | ||
| Mustard_and_Finnie | Jupyter Notebook | 10.3 MB | 153 | 2 | 136 | active | ||
| animal-welfare-assessment-grid Animal welfare assessment grid | Java | 10.1 MB | 55 | 5 | 651 | active | ||
| ai-blast-genotyping | Python | 9.3 MB | 115 | 5 | 29 | active | ||
| epidm Epidemiological Data Management | R | 8.7 MB | 625 | 16 | 103 | active CI | ||
| covid-pass-web The frontend web application for the NHS COVID Pass service | JavaScript | 8.1 MB | 9 | 6 | 226 | archived | ||
| hcaidcs An R package to interact with data from PHE's HCAI data capture system. https://hcaidcs.phe.org. | R | 7.3 MB | 185 | 7 | 427 | active | ||
| standards-qat UKHSA Standards for Quality Assurance Testing | JavaScript | 6.4 MB | 165 | 8 | 68 | active CI bot | ||
| ohid-tech-docs | Python | 6.4 MB | 130 | 2 | 63 | active CI | ||
| devops-terraform-modules UKHSA Terraform Modules to deliver a IaC self-service platform. Repo managed by devops-github-re | HCL | 6.0 MB | 355 | 17 | 110 | active CI | ||
| active10-cms-public | Python | 5.9 MB | 77 | 8 | 355 | active CI docker | ||
| nsc-recommendationsp | Python | 5.5 MB | 1,473 | 44 | 478 | active CI docker | ||
| active10-ios-public | Swift | 4.5 MB | 1 | 1 | 1,030 | active | ||
| active10-android-public | Kotlin | 3.7 MB | 1 | 1 | 1,640 | active | ||
| COVID-19-app-Android-BETA Source code of the Beta of the NHS COVID-19 Android app | Kotlin | 3.3 MB | 1,152 | 33 | 452 | archived CI docker | ||
| healthcheck | R | 3.2 MB | 1 | 1 | 17 | active | ||
| ModellingInfectionFatalityRatiosH5N1 This repository contains the R scripts, Stan scripts and Excel data sheets used in the publicati | R | 2.9 MB | 4 | 1 | 11 | active | ||
| inclusive-design-tool | JavaScript | 2.9 MB | 62 | 7 | 138 | active | ||
| covid-pass-verifier The COVID Pass Verifier app is the official NHS COVID Pass Verifier for England and Wales. NHS C | C# | 2.6 MB | 44 | 13 | 420 | archived | ||
| gpha-mscape-taxaplease An application for NCBI taxonomy wrangling | Python | 2.4 MB | 88 | 6 | 98 | active CI docker | ||
| statistics-production-hub A hub to host our best practice guidance resources. | Ruby | 2.4 MB | 19 | 6 | 82 | active | ||
| standards-api UKHSA API design guidelines. | TypeScript | 2.3 MB | 454 | 16 | 133 | active CI bot | ||
| COVID-19-app-Documentation-BETA Documentation relating to the Beta of the NHS COVID-19 app | - | 2.0 MB | 15 | 3 | 14 | archived | ||
| Sentinel_Selection_Using_Network_Analysis Exploiting network analysis to create a novel sentinel surveillance system for efficient, rapid | R | 2.0 MB | 10 | 1 | 13 | active | ||
| boostswift-public | C++ | 1.7 MB | 1 | 1 | 1,969 | archived | ||
| gene_finder | Python | 1.6 MB | 61 | 6 | 16 | active | ||
| SIRA | Jupyter Notebook | 1.3 MB | 21 | 5 | 15 | active | ||
| UKPID-Backend Public mirror of the UKPID Backend application currently in development by Juicy Media. | PHP | 1.2 MB | 86 | 6 | 302 | active docker | ||
| UKPID-Frontend Public mirror of the UKPID Desktop application currently in development by Juicy Media. | Vue | 1.2 MB | 34 | 3 | 272 | active | ||
| within-patient-pOXA48-conjugation An analysis on Plasmid conjugation for within-patient plasmid diversity | HTML | 879.6 kB | 16 | 1 | 15 | active | ||
| standards-org UKHSA organisation standards | JavaScript | 799.7 kB | 198 | 6 | 60 | active CI bot docker | ||
| ntbs-nhs-razor-tags A fork of https://github.com/nhsuk/frontend-dotnetcore introducing some tweaks. | C# | 746.5 kB | 72 | 15 | 205 | active | ||
| phds | HTML | 684.0 kB | 14 | 3 | 35 | active | ||
| cherami mSCAPE kubernetes orchestration module for downstream pathogen pipelines | Python | 644.1 kB | 300 | 6 | 47 | active CI docker | ||
| PHEnix Public Health England SNP calling pipeline. | Python | 602.1 kB | 373 | 10 | 122 | active | ||
| gaen_data-public | - | 544.8 kB | 1 | 1 | 29 | archived | ||
| standards-tech-radar UKHSA development technology radar | JavaScript | 540.7 kB | 46 | 4 | 33 | active CI bot | ||
| standards-template Template for standards documentation repositories | JavaScript | 531.5 kB | 76 | 4 | 39 | active CI bot | ||
| gpha-mscape-nf-contamination-reports Negative Control summary reports and per site. | Python | 523.3 kB | 247 | 7 | 23 | active | ||
| phe-bioinformatics.github.io | HTML | 502.8 kB | 67 | 1 | 21 | active | ||
| active10-backend | Python | 473.1 kB | 447 | 17 | 136 | active CI docker | ||
| devops-hello-world-front Frontend component of the DevOps example project. Repo managed by devops-github-repos | TypeScript | 468.0 kB | 56 | 6 | 31 | active CI docker | ||
| riskscore-kt-public | Kotlin | 425.0 kB | 1 | 1 | 83 | archived | ||
| standards-development Development standards for engineering teams | JavaScript | 406.5 kB | 97 | 11 | 51 | active CI bot | ||
| covid-pass-backend The backend applications and infrastructure for the NHS COVID Pass service | C# | 395.3 kB | 9 | 8 | 539 | archived docker | ||
| gpha-ai-mutation-library Library stores tables for avian influenza mutations of concern. | Python | 378.9 kB | 270 | 5 | 73 | active | ||
| riskscore-swift-public | Swift | 375.8 kB | 2 | 1 | 84 | archived | ||
| standards-wow UKHSA Ways of Working Standards | JavaScript | 363.5 kB | 36 | 5 | 39 | active CI bot | ||
| gpha-mscape-chimera-synteny A script that generates a HTML report with synteny plots, given CLIMB IDs as input | Python | 330.8 kB | 29 | 3 | 16 | active CI docker | ||
| devops-github-reusable-workflows Repo containing Github Reusable Workflows. Repo managed by devops-github-repos | - | 266.2 kB | 362 | 9 | 26 | active CI | ||
| standards-cloud-engineering UKHSA Cloud Engineering Standards | JavaScript | 264.2 kB | 36 | 4 | 39 | active CI bot | ||
| gpha-climb-sars-cov2-lineage-line-list | Python | 241.7 kB | 205 | 13 | 20 | active CI docker | ||
| gpha_mpox_kmer_typing | Python | 235.5 kB | 49 | 1 | 30 | active docker | ||
| fastq-factory | Ruby | 178.2 kB | 60 | 1 | 18 | active | ||
| gpha-mscape-orangebox-claspar ClasPar: the friendly classification parser that parses, filters and publishes analysis tables u | Python | 177.2 kB | 39 | 4 | 25 | active CI docker | ||
| gpha-mscape-onyx-analysis-helper A repository containing helper functions to interact with onyx analysis functionality. | Python | 174.1 kB | 177 | 6 | 20 | active CI docker | ||
| snapper3 partial reimplementation of snapperdb | Python | 170.0 kB | 139 | 1 | 31 | active | ||
| covid-pass-letter-frontend The frontend web application for the NHS COVID Pass letter service | C# | 158.7 kB | 9 | 6 | 188 | archived | ||
| devops-terraform-example-project Example for demonstrating ECS-based project created using IaC. Repo managed by devops-github-rep | HCL | 134.1 kB | 112 | 4 | 52 | active CI | ||
| emm-typing-tool Group A streptococci emm typing tool for NGS data | Python | 131.1 kB | 12 | 2 | 11 | active | ||
| active10-databricks | Python | 130.0 kB | 117 | 5 | 20 | active | ||
| gnsepinf_research_publication Code for "Characteristics and factors associated with mortality of infants with Gram-negative ba | R | 129.0 kB | 6 | 1 | 140 | active | ||
| devops-hello-world-api API component of the DevOps example project. Repo managed by devops-github-repos | Python | 126.0 kB | 16 | 1 | 29 | active CI docker | ||
| covid-pass-letter-backend The backend applications and infrastructure for the NHS COVID Pass letter service | C# | 118.8 kB | 8 | 6 | 189 | archived | ||
| gpha-mscape-orangebox-virus-reclassification Virus reclassification NextFlow pipeline | Python | 112.6 kB | 61 | 2 | 27 | active CI docker | ||
| gpha-mscape-sample-qc | Python | 111.6 kB | 105 | 5 | 21 | active CI docker | ||
| winter-2023-24-respiratory-forecasts Repository holding the operational code used to forecast COVID, Influenza & RSV over winter 2023 | R | 110.6 kB | 3 | 2 | 87 | active | ||
| variant_definitions | - | 99.3 kB | 69 | 9 | 39 | active | ||
| gpha-mscape-nf-strep-pneumo Nextflow pipeline for characterisation of Streptococcus pneumoniae in metagenomic samples | Python | 97.3 kB | 174 | 4 | 31 | active CI | ||
| forwardlook An R pacakge to scrape statistics announcement information from GOV.UK | R | 92.2 kB | 10 | 2 | 21 | active | ||
| devops-github-actions Repo containing reusable Github Actions. Repo managed by devops-github-repos | - | 86.0 kB | 74 | 7 | 34 | active CI docker | ||
| ena_submission | Python | 70.7 kB | 63 | 3 | 12 | active | ||
| covid-19-app-configuration-public | Swift | 68.6 kB | 3 | 1 | 27 | archived | ||
| devops-application-cicd | Python | 55.3 kB | 32 | 2 | 20 | active CI docker | ||
| gpha-mscape-nf-orange-box-public Nextflow workflow for mSCAPE sample processing through the Orange Box. | Python | 53.2 kB | 24 | 2 | 38 | active CI docker | ||
| ggbreak One-function R package for adding a y-axis break symbol to a ggplot object | R | 51.2 kB | 24 | 3 | 19 | active | ||
| mscape-template Template repository containing key files required for mSCAPE projects | Python | 50.2 kB | 51 | 4 | 15 | active CI docker | ||
| devops-terraform-standard-alarms Terraform module containing standard alarms | HCL | 49.2 kB | 43 | 2 | 23 | active CI | ||
| devops-terraform-template . Repo managed by devops-github-repos | - | 48.1 kB | 42 | 4 | 62 | active CI | ||
| devops-terraform-ci Container image used to run CI pipelines. Repo managed by devops-github-repos | Shell | 47.1 kB | 41 | 10 | 12 | active CI docker | ||
| gpha-mscape-taxaplease-container A repository for the taxaplease container, which assigns taxa information. | Python | 45.1 kB | 44 | 3 | 20 | active CI docker | ||
| inclusive-design-team | - | 44.0 kB | 49 | 1 | 12 | active | ||
| gpha-mscape-nf-CSI Pipeline to analyse clinical metagenomic samples | Python | 42.0 kB | 11 | 3 | 33 | active CI docker | ||
| s3-sync-action 🔄 GitHub Action to sync a directory with a remote S3 bucket 🧺 | Shell | 42.0 kB | 39 | 7 | 5 | archived docker | ||
| devops-terraform-rds-postgresql-aurora | HCL | 34.8 kB | 24 | 1 | 14 | active CI | ||
| TestResults | HTML | 32.8 kB | 11 | 2 | 2 | active | ||
| devops-phe-alarms-lambdas | Python | 32.8 kB | 14 | 1 | 20 | active CI | ||
| risk_scoring_nhs_covid19_app | R | 31.7 kB | 3 | 3 | 13 | active | ||
| gpha-mscape-orangebox-profiler Profiler: assign profiles to classified taxa. For use in the Orange Box. | Python | 29.7 kB | 9 | 2 | 15 | active CI docker | ||
| ssi-repo-test testing the use of git-repo-filter | TSQL | 26.6 kB | 9 | 2 | 10 | active | ||
| Rnanoflann | C++ | 25.6 kB | 13 | 4 | 16 | active | ||
| bayesint Repository containing code for calculating a credible interval of a ratio | Python | 25.6 kB | 28 | 4 | 16 | active | ||
| devops-terraform-public-alb | HCL | 23.6 kB | 9 | 1 | 11 | active CI | ||
| UKHSA-pubhealthbench Evaluation code for the PubHealthBench benchmark. | Python | 17.4 kB | 7 | 4 | 8 | active | ||
| gpha-mscape-fastq-read-stats-nf A nextflow pipeline wrapping a tool that generates basic statistics given a fastq.gz as input | Nextflow | 17.4 kB | 6 | 2 | 14 | active | ||
| gpha-mscape-genomad-nf A nextflow pipeline wrapping geNomad | Nextflow | 15.4 kB | 4 | 2 | 10 | active | ||
| better-health-auth-keycloak | - | 14.3 kB | 1 | 1 | 1 | active | ||
| SmallpoxSomaliaReleased | Jupyter Notebook | 13.3 kB | 3 | 1 | 3 | active | ||
| gpha-mscape-fastq-read-stats A tool that generates basic statistics given a fastq.gz as input | Python | 13.3 kB | 4 | 2 | 11 | active | ||
| renovate POC for centralised self-hosted Renovate using Github Actions | - | 13.3 kB | 12 | 2 | 6 | active CI | ||
| CDI_LR_external External repository for sharing CDI logistic regression code | R | 12.3 kB | 3 | 2 | 6 | active | ||
| avian_influenza_scenario_calculations Python code for the scenario calculations as part of the avian influenza tech briefing | Jupyter Notebook | 12.3 kB | 2 | 1 | 4 | active | ||
| gpha-mscape-aletheia-seq Application to confirm the presence of species specific loci in fastq data | Python | 7.2 kB | 1 | 1 | 13 | active CI docker | ||
| gpha-mscape-contamination Tool to gather and plot the negative control data and create summary HTML reports, and reports p | Python | 7.2 kB | 2 | 2 | 13 | active CI docker | ||
| distroless-base A collection of distroless base container images used by UKHSA applications | Dockerfile | 2.0 kB | 1 | 1 | 4 | active CI docker | ||
| Burden-of-Infectious-Diseases-Dashboard Open sourcing code used in the Burden of Infectious Diseases Dashboard | - | 1.0 kB | 3 | 2 | 1 | active | ||
| hepatitis-of-unknown-aetiology | - | 1.0 kB | 2 | 2 | 1 | active | ||
| influenza-forecast-paper-hgam-2022 Repository for the code used within the paper titled: "Forecasting influenza hospital admissions | - | 1.0 kB | 1 | 1 | 2 | active | ||
| ukhsa-project-template A cookie cutter template to set up a data science folder structure with git collaboration in min | - | 1.0 kB | 1 | 1 | 2 | active | ||
| SDLC | - | 0 B | 0 | 0 | 0 | active | ||
| Test-PublicRepo-TOBEDELETED | - | 0 B | 0 | 0 | 0 | active | ||
| UKHSAConferenceWebsite23 | - | 0 B | 0 | 0 | 0 | active | ||
| devops-base-images A collection of base container images used by UKHSA applications | - | 0 B | 1 | 1 | 1 | active | ||
| epi-ensemble-MTP-journal-code This code produces the results discussed in a paper I am submitting to the Proceedings of the Ro | - | 0 B | 0 | 0 | 0 | active | ||
| gpha-mscape-amr-report AMR Report for mSCAPE data | - | 0 B | 0 | 0 | 0 | active | ||
| gpha-mscape-reference-removal Removal of reference sequence data from metagenomic datasets | - | 0 B | 1 | 1 | 1 | active | ||
| terraform-github-repository Terraform module to configure GitHub repositories | - | 0 B | 0 | 0 | 0 | active |