6  Project Organization

If you would like a video overview of how to organize a project using R Studio, I recommend Ming “Tommy” Tang’s tutorial on YouTube, “How to Organize a Computational Biology Project”. In his tutorial he references an excellent reference on project organization, “A Quick Guide to Organizing Computational Biology Projects” by Noble (2009).

Note

In RStudio, you should create a “New Project,” which creates both a project folder and a .Rproj file (which sets the path for your project working directory). You should use the here package to easily build paths to files in a more reliable fashion than using setwd().

Bash Commands to Create Folder Directory Structure for Your R Project

Once you have created your New Project in RStudio and are in your-r-project-folder in the Terminal. You can create your README.md file and your sub-folder directory structure.

touch README.md
mkdir data doc scripts bin outputs

Once you have downloaded your raw data to your data folder, you should make the contents of the data folder read-only (non-editable) with the following command: chmod u-w -R data/

Noble, William Stafford. 2009. “A Quick Guide to Organizing Computational Biology Projects.” Edited by Fran Lewitter. PLoS Computational Biology 5 (7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424.