Code to reproduce scRNA-seq analysis in Fanti et al., 2022

The analysis performed is structured as follows (arrows indicate dependencies)

The matching R environment is stored in renv.lock and can be restored using the renv package.

Raw and processed data are available on GEO and will be made publicly available upon publication. To reproduce the analysis, processed data should be placed in data/day_<1/3>.

Please make sure that other folders used throughout the analysis exist before running the scripts.