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

本数据包包含所有可复现研究论文《grandR：一款用于核苷酸转化测序数据分析的综合工具包》中分析流程的R笔记本。该压缩包的data文件夹内存储有多个rds格式文件，其中包含模拟与真实SLAM测序（SLAM-seq）数据集的grandR对象。用户可删除这些文件，并通过两种方式重新生成：其一，直接"编织（knit）"对应笔记本，该操作会生成当前笔记本所需的全部数据并保存至data文件夹；其二，执行generateAllDataFiles.R脚本（执行命令为"Rscript generateAllDataFiles.R"），该脚本将生成所有缺失的rds文件。本数据包还包含多个R Markdown（Rmd）格式笔记本，"编织（knit）"这些笔记本即可生成该研究论文中的全部图表。若缺少rds数据文件，运行过程将较为缓慢。knit_all.bash：执行该脚本可一键"编织"所有笔记本。clean.bash：用于清除"编织"笔记本后产生的全部输出内容。