Pinned Repositories
covid-19_instant_tracing
Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. More details on our website:
covid-19_shiny
Code for "Digital contact tracing for SARS-COV-2" shiny app
EpiLine
Bayesian Modelling in Epidemiology Case Line Lists
HIV-phyloTSI
Estimate time since infection (TSI) from HIV deep-sequencing data
Isle_of_Wight
Data and source code for reproducing the analysis of paper:
OpenABM-Covid19
OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic
OpenABM-Covid19-model-paper
Figures for the paper describing the OpenABM-Covid19 model
phyloscanner
Phylogenetics between and within hosts at once, all along the genome.
POPART-IBM
C code of the individual-based model developed as part of the HPTN071 (PopART) trial
VariantREstimate
Estimate R(t) and relative transmissibility of multiple variants of a virus.
Pandemic Sciences Institute: Pathogen Dynamics Group's Repositories
BDI-pathogens/OpenABM-Covid19
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/covid-19_instant_tracing
Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. More details on our website:
BDI-pathogens/phyloscanner
Phylogenetics between and within hosts at once, all along the genome.
BDI-pathogens/EpiLine
Bayesian Modelling in Epidemiology Case Line Lists
BDI-pathogens/covid-19_shiny
Code for "Digital contact tracing for SARS-COV-2" shiny app
BDI-pathogens/Isle_of_Wight
Data and source code for reproducing the analysis of paper:
BDI-pathogens/OpenABM-Covid19-model-paper
Figures for the paper describing the OpenABM-Covid19 model
BDI-pathogens/POPART-IBM
C code of the individual-based model developed as part of the HPTN071 (PopART) trial
BDI-pathogens/HIV-phyloTSI
Estimate time since infection (TSI) from HIV deep-sequencing data
BDI-pathogens/nhs_covid_app_evaluation
BDI-pathogens/VariantREstimate
Estimate R(t) and relative transmissibility of multiple variants of a virus.
BDI-pathogens/LocalCovidTracker
Code for the shiny app LocalCovidTracker https://bdi-pathogens.shinyapps.io/LocalCovidTracker/
BDI-pathogens/stan_epi_tutorial
BDI-pathogens/covid19_r_map_ew
Illustration of a map of England and Wales in R using data on R(t) from LocalCovid19Tracker
BDI-pathogens/RTreePlot
An R package for an interactive transmission tree plotter.
BDI-pathogens/cleanr
cleanr package used in the data cleaning and recoding of PC data
BDI-pathogens/hiv_spvl_fitness
Supplementary files for HIV SPVL fitness paper
BDI-pathogens/PopART_docs
BDI-pathogens/popart_pre_post_unblinding_figures
BDI-pathogens/seq_dbutils
MySQL database utilities for the sequencing databases
BDI-pathogens/ShiverCovid
Covid Illumina sequence data processing pipeline