cobeylab

Rt_estimation

Code to test Rt estimates against synthetic data

Influenza-immune-dynamics

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

epidemic-deconvolution

Example code for deconvolving epidemic time series

FluVE_repeatvac_public

flu_strain_compare

Visualizing mutations and PNGS changes between two strains

FluAImprinting

Data and code for Arevalo et al., 2019

OAS-strain-replacement

Code for reproducing results in "A speed limit on serial strain replacement from Original Antigenic Sin"

antigen-vaccine

antigenic-maps

Code to infer antigenic maps from titer panel data

data-emporium

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

lab_handbook

Nextstrain-on-HPC

How to install and run Nextstrain in HPC environments

psc_repertoire

Analysis of B cell repertoires from patients with primary sclerosing cholangitis (PSC). Collaboration led by Dustin Shaw and Bana Jabri

rough_rt

Code for rough estimates from data

sitrep

v_gene_selection

V gene usage in mice infected with flu.

vaccine-manuscript

covid_IL

digital-repeatability

Materials for digital repeatability training

imprinting

Code to reconstruct influenza imprinting probabilities from 1918 to present

version-control-training

Materials for version control training

code-structure-training

Materials for code structure training

covid19-forecast-hub

Projections of COVID-19, in standardized format

egg_antibodies

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

evolution_of_mutability

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

Flu-Middle-aged

Data and analyses for Gouma et al

hong_kong_publc_data_site

Hong Kong flu data

imprinting_tutorial_bookdown

Bookdown document with a lesson on calculating imprinting probabilities

population_immunity_predicting_flu

refit_antigenic_seniority

Code to refit the models in Lessler et al. 2012, PLOS Pathogens