The R code to accompany the manuscript “A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system” by Mark Reglinski, Quenton W. Hurst, David J. Williams, Marek Gierlinski, Alp Tegin Şahin, Katharine Mathers, Adam Ostrowski, Megan Bergkessel, Ulrich Zachariae, Samantha J. Pitt and Sarah J. Coulthurst.
The R code in this repository uses renv and targets for reproducibility. renv is used to reproduce the R environment:
install.packages("renv")
renv::restore()
Next, the targets pipeline is invoked with the following command:
targets::tar_make()
Finally, the HTML report, including all figures, can be created with:
quarto::quarto_render("doc/report.qmd")
The HTML file will be created in folder doc.