This repository contains all code for the NIAID CEIRR Training Program Antigenic Cartography Workshop July 9-10, 2025
We will be working with free software.
The workshop is run in R. Please make sure you have a working installation of R on your computer. Instructions for download and installation can be found on the official R website: https://cran.r-project.org
Make sure you install the correct R for your operating system.
To install the ablandscapes package, you need to have development tools installed for your operating system. Instructions
are linked on the R page. Here are the instructions to install the tools for MacOS, XCode and gfortran are needed: https://mac.r-project.org/tools/
If installation issues occur, it is often because the R version and the development tools version do not match. We recommend installing the most recent version of both and updating R if necessary.
To screenshot antibody landscapes, we will use a package that requires installation of Google Chrome on your device.
We also recommend installing RStudio as it provides an accessible user interface: https://posit.co/products/open-source/rstudio/
Once you have everything installed, please open a session in RStudio and run the script code/00_installation.R to install all
packages that we will be using throughout the workshop.
For a python interface to Racmacs, please follow the instructions here: https://github.com/iAvicenna/PyRacmacs
The code for each session is in the code directory and numbered. We will provide working code for each
session in the same directory with the appendix _solution.Rmd but encourage
participants to try each task by themselves first.
