Code availability for "RNase-based defence preserves methicillin susceptibility in Staphylococcus aureus": SadR/ST188

The code used in this study This archive contains the notebooks/scripts and minimal input tables used to generate the main and supplementary figure panels for our manuscript on SadR in Staphylococcus aureus ST188. Directory structure code_availability/ Fig.1/, Fig.2/, Fig.4/, Fig.5/: figure-specific code and input tables supplementary_fig/: code and input tables for supplementary figures How to run Python notebooks (.ipynb): open in JupyterLab/Jupyter Notebook and run cells from top to bottom. R Markdown (.Rmd): knit in RStudio or run via rmarkdown::render(). Notes CSV files in this archive are figure-level inputs (and/or intermediate tables) used for plotting. Large raw datasets (e.g., genome assemblies/FASTA files) are available through the public repositories and accession numbers provided in the manuscript’s Data Availability section. PDF files are example outputs for reference. Figures were generated from the code at the time of submission; in a small number of cases, minor graphical adjustments (e.g., layout/label positioning) were made in Adobe Illustrator for publication-quality presentation. Contact Kohei Kondo ([e-mail])本研究使用的代码 本归档文件包含用于生成我们关于金黄色葡萄球菌（Staphylococcus aureus）ST188中SadR的研究手稿的主图与补充图面板的Notebook、脚本及最小化输入表格。 目录结构 code_availability/ Fig.1/、Fig.2/、Fig.4/、Fig.5/：对应单张图表的专属代码与输入表格 supplementary_fig/：用于生成补充图表的代码与输入表格 运行方法 Python Notebook（.ipynb）：在JupyterLab/Jupyter Notebook中打开，并按从上到下的顺序运行单元格。 R Markdown（.Rmd）：可在RStudio中进行编织，或通过rmarkdown::render()命令运行。 备注 本归档文件中的CSV文件为绘图所用的图表级输入文件（及/或中间表格）。 大型原始数据集（例如基因组组装文件/FASTA格式文件）可通过手稿数据可用性部分提及的公共数据库与登录号获取。 PDF文件为可供参考的示例输出结果。所有图表均基于投稿时的代码生成；少数情况下，为达到出版级展示效果，会使用Adobe Illustrator对图形进行微调（例如调整布局与标签位置）。 联系方式 近藤航平（Kohei Kondo），邮箱：[e-mail]