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@BDI-pathogens Pandemic Sciences Institute: Pathogen Dynamics Group

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    26 repositories

    • OpenABM-Covid19

      Public
      OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic
      covid-19
      Python
      •
      GNU General Public License v3.0
      •75•123•13•9•Updated Oct 9, 2025Oct 9, 2025

    • EpiLine

      Public
      Bayesian Modelling in Epidemiology Case Line Lists
      R
      •
      GNU General Public License v3.0
      •4•14•2•1•Updated Oct 7, 2025Oct 7, 2025

    • oxdaepyutils

      Public
      Python utilities from the Oxford University Pandemic Sciences Institute (PSI) Data Analytics & Epidemiology (DAE) research group
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 2, 2025Oct 2, 2025

    • rPQ

      Public
      Evaluation of prevalence in test data sets using classifiers trained on data sets with different prevalences.
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • BEEHIVE_GWAS

      Public
      Code and minimal dataset for BEEHIVE GWAS
      R
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • EpiAgeVar

      Public
      Estimating R(t) by age group in the presence of multiple variants
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • contactsim

      Public
      Python Bluetooth device contact simulator
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 3, 2025Apr 3, 2025

    • stan_epi_tutorial

      Public
      R
      •1•1•0•0•Updated Mar 19, 2025Mar 19, 2025

    • seq_dbutils

      Public
      MySQL database utilities for the sequencing databases
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • POPART-IBM

      Public
      C code of the individual-based model developed as part of the HPTN071 (PopART) trial
      C
      •
      GNU General Public License v3.0
      •4•5•0•1•Updated Oct 11, 2024Oct 11, 2024

    • HIV-phyloTSI

      Public
      Estimate time since infection (TSI) from HIV deep-sequencing data
      Python
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Oct 3, 2024Oct 3, 2024

    • phyloscanner

      Public
      Phylogenetics between and within hosts at once, all along the genome.
      HTML
      •
      GNU General Public License v3.0
      •14•50•9•1•Updated Oct 2, 2024Oct 2, 2024

    • ShiverCovid

      Public
      Covid Illumina sequence data processing pipeline
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jul 15, 2024Jul 15, 2024

    • covid19_r_map_ew

      Public
      Illustration of a map of England and Wales in R using data on R(t) from LocalCovid19Tracker
      R
      •1•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • LocalCovidTracker

      Public
      Code for the shiny app LocalCovidTracker https://bdi-pathogens.shinyapps.io/LocalCovidTracker/
      R
      •
      MIT License
      •1•1•2•0•Updated May 9, 2023May 9, 2023

    • popart_pre_post_unblinding_figures

      Public
      0•0•0•0•Updated Oct 10, 2022Oct 10, 2022

    • hiv_spvl_fitness

      Public
      Supplementary files for HIV SPVL fitness paper
      R
      •0•0•0•0•Updated Feb 9, 2022Feb 9, 2022

    • VariantREstimate

      Public
      Estimate R(t) and relative transmissibility of multiple variants of a virus.
      C++
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Jan 21, 2022Jan 21, 2022

    • OpenABM-Covid19-model-paper

      Public
      Figures for the paper describing the OpenABM-Covid19 model
      Jupyter Notebook
      •0•4•0•0•Updated Jun 23, 2021Jun 23, 2021

    • nhs_covid_app_evaluation

      Public
      R
      •3•3•0•0•Updated May 27, 2021May 27, 2021

    • RTreePlot

      Public
      An R package for an interactive transmission tree plotter.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 21, 2021May 21, 2021

    • covid-19_instant_tracing

      Public
      Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. More details on our website:
      oxfordcoronaviruscovid-19
      12•101•4•0•Updated Apr 28, 2021Apr 28, 2021

    • Isle_of_Wight

      Public
      Data and source code for reproducing the analysis of paper:
      Stata
      •
      Creative Commons Attribution 4.0 International
      •1•4•0•0•Updated Oct 14, 2020Oct 14, 2020

    • covid-19_shiny

      Public
      Code for "Digital contact tracing for SARS-COV-2" shiny app
      R
      •
      MIT License
      •3•10•0•0•Updated Oct 14, 2020Oct 14, 2020

    • PopART_docs

      Public
      0•0•0•0•Updated Jul 6, 2020Jul 6, 2020

    • cleanr

      Public
      cleanr package used in the data cleaning and recoding of PC data
      R
      •
      Other
      •4•0•0•0•Updated Mar 30, 2017Mar 30, 2017