This repository collects the code for the analyses presented in the paper: Unravelling the collateral damage of antibiotics on gut bacteria.
The accompanying data needed to reproduce the results are available through Zenodo:
In order to reproduce the results presented in the paper, you can use the provided scripts. All analyses were performed using R version 4.1.0 and the needed packages can be installed with the provided renv.lock file, since this project uses the project environment management package renv. You can check out the documentation for more information: renv tutorial.
After installing all required packages, you can automatically download the data by executing the setup.R script in the utils folder.
For any questions or comments, please contact the corresponding author or l.maier [at] uni-tuebingen.de.