Comparative Analysis of SARS-CoV-2 Neutralization Titers across Assays and Human and Animal Sera

This repository contains the raw data and code to reproduce the analyses presented in Comparative Analysis of SARS-CoV-2 Neutralization Titers across Assays and Human and Animal Sera.

Directory structure

main_figures: Subdirectories for each main figure containing the code to produce each figure, as well as the main figures themselves.

som_figures: Subdirectories for SOM figures containing the code to produce each figure, as well as the SOM figures themselves.

data: Raw data and code to produce data used for plotting.

code: Code and helper functions.

Dependencies

All dependencies are listed in the DEPENDENCIES file. Apart from the dependencies available through CRAN, the following packages specific to antigenic cartography and titer analysis are required:

Racmacs

Available from github.com/shwilks/Racmacs, or through CRAN.

titertools

Available from github.com/shwilks/titertools.

Generating data and figures

To re-generate data associated with figures, run code/generate_data.R.

To re-generate the figures, run code/generate_figures.R.