Ho et al. CRISPR simulation

Files to recreate CRISPR simulation from Ho et al. 2025, including: CRISPRi_stats.Rmd Quantify variation from existing CRISPRi screen data using prolif.lib2.run2.count_normalized.txt, prolif.lib2.run2.gene_summary.txt, and prolif.lib2.run2.sgrna_summary.txt. Dataset (A-J) directories R Markdown files titled generate_fake_screen_data.Rmd were used to generate simulated CRISPR screen count tables for ten independent replicates, which are found in the directory count_tables. Count tables were analyzed using mageck test with and without the --control-sgrna option, and the resulting gene summaries of these analyses are in the directories mageck_output_control and mageck_output_no_control, respectively. precision_recall_plots.Rmd Plot the precision and recall of the simulated CRISPR screens based on gene summary output from mageck test.用于复现Ho等人2025年研究中成簇规律间隔短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats，CRISPR）模拟实验的文件如下： CRISPRi_stats.Rmd：基于prolif.lib2.run2.count_normalized.txt、prolif.lib2.run2.gene_summary.txt及prolif.lib2.run2.sgrna_summary.txt三份现有CRISPR干扰（CRISPR interference, CRISPRi）筛选数据，量化实验变异程度。 数据集（A-J）目录 名为generate_fake_screen_data.Rmd的R Markdown脚本可生成10组独立重复的模拟CRISPR筛选计数表，相关文件存储于count_tables目录中。 计数表分别在添加与不添加`--control-sgrna`参数的条件下，通过全基因组CRISPR-Cas9敲除模型分析工具（Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout, MAGECK）test进行分析，两类分析得到的基因汇总结果分别存储于mageck_output_control与mageck_output_no_control目录中。 precision_recall_plots.Rmd：基于MAGECK test输出的基因汇总结果，绘制模拟CRISPR筛选实验的精确率-召回率曲线。