R notebooks to reproduce all analyses from the manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis"

This package contains all R notebooks to reproduce the analyses from our manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis".

In the zip file you find

• several rds files in the data folder: They contain grandR objects of both simulated and real SLAM-seq data sets. You can delete them and create them again by either just "knitting" the notebooks (which will generate all data necessary for this notebook and save it into the data folder), or by executing the generateAllDataFiles.R script ("Rscript generateAllDataFiles.R"), which will  generate all rds files that do not exist).
• several R notebooks (Rmd): "Knitting" them will generate all figures from the manuscript. Without the data files (rds), this will be slow!
• knit_all.bash: Execute to "knit" all notebooks
• clean.bash: Clear the output of "knitting" the notebooks