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

DOI10.5281/zenodo.7843048Zenodo7843048MaRDI QIDQ6690169FDOQ6690169

Dataset published at Zenodo repository.

Florian Erhard

Publication date: 20 September 2022

Copyright license: Creative Commons Attribution 4.0 International

Description

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

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