bdi-pathogens Goto Github PK

cleanr

cleanr package used in the data cleaning and recoding of PC data

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

covid19_r_map_ew

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

epiline

Bayesian Modelling in Epidemiology Case Line Lists

hiv-phylotsi

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

hiv_spvl_fitness

Supplementary files for HIV SPVL fitness paper

isle_of_wight

Data and source code for reproducing the analysis of paper:

localcovidtracker

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

nhs_covid_app_evaluation

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

popart_docs

popart_pre_post_unblinding_figures

rtreeplot

An R package for an interactive transmission tree plotter.

seq_dbutils

MySQL database utilities for the sequencing databases

shivercovid

Covid Illumina sequence data processing pipeline

stan_epi_tutorial

variantrestimate

Estimate R(t) and relative transmissibility of multiple variants of a virus.