RigginsLabGU/Rmarkdown ? reverse-engineered prompt

I want a simple set of R Markdown analysis notebooks for two cancer data projects, one for SCANB and one for TCGA.

Each notebook should be ready to run from start to finish, with clear text explaining what each step is doing, and code chunks for loading data, cleaning it, doing the main analysis, making a few helpful plots, and summarizing the results in an easy to read way. Please keep it organized like something a researcher could open and follow without needing to rewrite much.

If anything depends on current R packages or best practices, look up the latest docs online and use sensible defaults. I’d like the output to feel polished and reproducible, with reasonable section headings, comments, and placeholders where the real data or study specific details would go.