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antigen

Simulating virus evolution and epidemiology

antigen-phylogeography

antigen-vaccine

antigenic-maps

Code to infer antigenic maps from titer panel data

bcell_id_pop_model

Repository for B-Cell population dynamical models of immunodominance

causality_manuscript

ccm-letter

code-structure-training

Materials for code structure training

covid19-forecast-hub

Projections of COVID-19, in standardized format

covid_il

data-emporium

A place to keep track of public or confidential datasets available to the Cobey Lab.

digital-repeatability

Materials for digital repeatability training

egg_antibodies

Analysis of non-templated insertions in glycan-binding antibodies of humans vaccinated with influenza

epidemic-deconvolution

Example code for deconvolving epidemic time series

evolution_of_mutability

Self-contained, publication-ready repository for the evolution of mutability project.

flu-middle-aged

Data and analyses for Gouma et al

flu-vaccine-sieve

flu_response_aging

Collaboration with Patrick's Wilson's group, led by Carole Henry: Aged individuals no longer efficiently adapt their B cell responses to influenza

flu_strain_compare

Visualizing mutations and PNGS changes between two strains

fluaimprinting

Data and code for Arevalo et al., 2019

fluve_repeatvac_public

gcdynamics

Model of germinal center B-cell affinity maturation.

h3n2_glycosylation

hong_kong_publc_data_site

Hong Kong flu data

hpv-model

imprinting

Code to reconstruct influenza imprinting probabilities from 1918 to present

imprinting_tutorial_bookdown

Bookdown document with a lesson on calculating imprinting probabilities

influenza-immune-dynamics

Code to accompany the manuscript "Age-specific differences in the dynamics of protective immunity to influenza"

influenza_phylogeography_manuscript

isotype_phylogenetics

This repository contains analyses for a collaboration led by Patrick Wilson's lab on the phylogenetic relatedness of B cells with different isotypes.