Pinned Repositories
antigen-phylogeography
epidemic-deconvolution
Example code for deconvolving epidemic time series
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.
HPV-model
Influenza-immune-dynamics
Code to accompany the manuscript "Age-specific differences in the dynamics of protective immunity to influenza"
pyembedding
Python implementation of nonlinear embedding methods
Rt_estimation
Code to test Rt estimates against synthetic data
cobeylab's Repositories
cobeylab/Rt_estimation
Code to test Rt estimates against synthetic data
cobeylab/Influenza-immune-dynamics
Code to accompany the manuscript "Age-specific differences in the dynamics of protective immunity to influenza"
cobeylab/epidemic-deconvolution
Example code for deconvolving epidemic time series
cobeylab/FluVE_repeatvac_public
cobeylab/flu_strain_compare
Visualizing mutations and PNGS changes between two strains
cobeylab/FluAImprinting
Data and code for Arevalo et al., 2019
cobeylab/OAS-strain-replacement
Code for reproducing results in "A speed limit on serial strain replacement from Original Antigenic Sin"
cobeylab/antigen-vaccine
cobeylab/antigenic-maps
Code to infer antigenic maps from titer panel data
cobeylab/data-emporium
A place to keep track of public or confidential datasets available to the Cobey Lab.
cobeylab/lab_handbook
cobeylab/Nextstrain-on-HPC
How to install and run Nextstrain in HPC environments
cobeylab/psc_repertoire
Analysis of B cell repertoires from patients with primary sclerosing cholangitis (PSC). Collaboration led by Dustin Shaw and Bana Jabri
cobeylab/rough_rt
Code for rough estimates from data
cobeylab/v_gene_selection
V gene usage in mice infected with flu.
cobeylab/vaccine-manuscript
cobeylab/covid_IL
cobeylab/digital-repeatability
Materials for digital repeatability training
cobeylab/imprinting
Code to reconstruct influenza imprinting probabilities from 1918 to present
cobeylab/version-control-training
Materials for version control training
cobeylab/code-structure-training
Materials for code structure training
cobeylab/covid19-forecast-hub
Projections of COVID-19, in standardized format
cobeylab/egg_antibodies
Analysis of non-templated insertions in glycan-binding antibodies of humans vaccinated with influenza
cobeylab/evolution_of_mutability
Self-contained, publication-ready repository for the evolution of mutability project.
cobeylab/Flu-Middle-aged
Data and analyses for Gouma et al
cobeylab/H5_titers_vs_imprinting
We ask if titers to H5 are more strongly associated with imprinting/year of birth than with age, in a collaboration led by the Hensey lab.
cobeylab/hong_kong_publc_data_site
Hong Kong flu data
cobeylab/imprinting_tutorial_bookdown
Bookdown document with a lesson on calculating imprinting probabilities
cobeylab/population_immunity_predicting_flu
cobeylab/refit_antigenic_seniority
Code to refit the models in Lessler et al. 2012, PLOS Pathogens