This is provided as a rough guide only. Some sections are suggestions, or else would only truly be necessary in the event of a project handover. Fill in / delete as appropriate.
Your first task is to rename the parent directory (currently ProjectFolder) to something which is clearly identifiable as your project.
All of the directory titles are also suggestions. Though the overall structure follows what we consider best practice, there is room for tweaks. I.e. perhaps the output folders tables or figures should be found in the parent directory and output should be removed. Else directories may be numbered (i.e. 01_install, 02_raw) to keep in the preferred order. There may also be project-specific directory structures required.
Similarly, markdowns/Jupyter notebooks/scripts/quarto markdowns should be numbered in the order that they are needed in the analysis.
Provide some details regarding what the project is, perhaps touching on the biological context. Providing some keywords (i.e. RNA-Seq, biomarkers, proteomics) may suffice.
Installation directions pertaining to scripts/resources provided in the install directory.
Instructions as to how to run the project.
Ideally there should be a master script/.rmd/.qmd/.R that can run the anlaysis from start to finish in the home directory. Details may be provided there.