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Pandemic Sciences Institute: Pathogen Dynamics Group

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  1. OpenABM-Covid19 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

    Python 115 75

  2. covid-19_instant_tracing 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:

    100 12

  3. phyloscanner phyloscanner Public

    Phylogenetics between and within hosts at once, all along the genome.

    HTML 47 14

  4. EpiLine EpiLine Public

    Bayesian Modelling in Epidemiology Case Line Lists

    R 13 4

  5. covid-19_shiny covid-19_shiny Public

    Code for "Digital contact tracing for SARS-COV-2" shiny app

    R 10 3

  6. POPART-IBM POPART-IBM Public

    C code of the individual-based model developed as part of the HPTN071 (PopART) trial

    C 4 4

Repositories

Showing 10 of 21 repositories
  • seq_dbutils Public

    MySQL database utilities for the sequencing databases

    BDI-pathogens/seq_dbutils’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 6, 2024
  • POPART-IBM Public

    C code of the individual-based model developed as part of the HPTN071 (PopART) trial

    BDI-pathogens/POPART-IBM’s past year of commit activity
    C 4 GPL-3.0 4 0 1 Updated Oct 11, 2024
  • HIV-phyloTSI Public

    Estimate time since infection (TSI) from HIV deep-sequencing data

    BDI-pathogens/HIV-phyloTSI’s past year of commit activity
    Python 3 GPL-3.0 0 1 0 Updated Oct 3, 2024
  • phyloscanner Public

    Phylogenetics between and within hosts at once, all along the genome.

    BDI-pathogens/phyloscanner’s past year of commit activity
    HTML 47 GPL-3.0 14 8 1 Updated Oct 2, 2024
  • ShiverCovid Public

    Covid Illumina sequence data processing pipeline

    BDI-pathogens/ShiverCovid’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Jul 15, 2024
  • EpiLine Public

    Bayesian Modelling in Epidemiology Case Line Lists

    BDI-pathogens/EpiLine’s past year of commit activity
    R 13 GPL-3.0 4 2 1 Updated May 18, 2024
  • covid19_r_map_ew Public

    Illustration of a map of England and Wales in R using data on R(t) from LocalCovid19Tracker

    BDI-pathogens/covid19_r_map_ew’s past year of commit activity
    R 0 1 0 0 Updated Jan 16, 2024
  • stan_epi_tutorial Public
    BDI-pathogens/stan_epi_tutorial’s past year of commit activity
    R 1 1 0 0 Updated Jan 12, 2024
  • 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

    BDI-pathogens/OpenABM-Covid19’s past year of commit activity
    Python 115 GPL-3.0 75 13 9 Updated Jul 23, 2023
  • LocalCovidTracker Public

    Code for the shiny app LocalCovidTracker https://bdi-pathogens.shinyapps.io/LocalCovidTracker/

    BDI-pathogens/LocalCovidTracker’s past year of commit activity
    R 1 MIT 1 2 0 Updated May 9, 2023
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