Pinned Repositories
baltic
baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longer receive updates, so any further development to baltic is going to happen at https://github.com/evogytis/baltic.
beta-cov
One-off nextstrain build for betacoronavirus
blotter
bedford lab research
global-migration
Analysis of global migration patterns of seasonal influenza viruses
ncov-phylodynamics
Phylodynamic estimation of nCoV incidence and prevalence
nextflu
Real-time tracking of influenza evolution
rt-from-frequency-dynamics
sars-like-cov
This is a one-off Nextstrain build for SARS-like coronaviruses
siv-cst
Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission
zika-seq
Pipelines to do MinION sequencing of Zika virus
Bedford Lab's Repositories
blab/blotter
bedford lab research
blab/rt-from-frequency-dynamics
blab/size-genetic-clusters
Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"
blab/cartography
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
blab/flu-forecasting
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
blab/evofr
Tools for evolutionary forecasting
blab/veme-2022
Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain
blab/adaptive-evolution
An atlas of continuous adaptive evolution in endemic human viruses
blab/ncov-early-outbreak
Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan
blab/cholera
blab/fitness-dynamics
Comparing fitness dynamics across SARS-CoV-2, influenza H3 and influenza H1
blab/mpox-dynamics
Phylodynamics of the 2022 mpox epidemic
blab/ncov-forecasting-fit
Assessing accuracy of fitness model forecasts
blab/pathogen-embed
Create reduced dimension embeddings for pathogen sequences
blab/popcast
Long-term forecasts for pathogen populations
blab/sars2-within-host-selection
Correlating within-host and between-host fitness in SARS-CoV-2
blab/ncov-escape
Nextstrain build for SARS-CoV-2 to calculate immune escape of circulating viruses
blab/phylo-kernel-public
Code and data for: "Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences".
blab/blotter-deploy
Script to build and deploy Bedford lab website
blab/flu-forecasting-delays
Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2
blab/loes-2024-neutralization-nextstrain
Phylogenetic analysis and visualization of H1N1pdm neutralization data from Loes et al. 2024
blab/measurements-panel
Manuscript and data describing joint visualization of influenza serology and phylogeny
blab/mers-evolution
blab/mers_skyline
analysis of updated MERS data via approximate structured coalescent approaches
blab/ncov-king-county
Local-scale phylodynamics of SARS-CoV-2 in King County, WA
blab/ncov-orf8
Positive selection for ORF8 knockout in SARS-CoV-2
blab/ncov-usa-mig
blab/perofsky-ili-antigenicity
Seasonal flu build for analysis of antigenic evolution in ILI data
blab/vscode-guide
A guide on practical uses for the popular text editor by members of the Bedford Lab
blab/welsh-escape-scores
Analysis of predictive value of escape scores from Welsh et al. 2023 experimental data