Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants
This repo contains data and code for the analyses presented in Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants, PNAS, 2024.
Rcivaclib and civaclib: R and Python code, respectively.
bin: Bin scripts
data: Raw data and code to generate antigenic maps.
figures: Code to generate the figures shown in the paper, as well as the resulting figures.
test: Tests.
All dependencies for R 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:
Available from github.com/shwilks/Racmacs, or through CRAN.
Available from github.com/shwilks/titertools.
Furthermore, for Python, the following libraries need to be installed: neutcurve, pandas, numpy.