D

Project Templates

It is very easy and convenient to put all the data, code, and outputs in the same folder. However, this convenience is negated by disadvantages of having a messy project folder. That is, putting everything into a single folder can easily lead to a folder on your computer with tens or hundreds of files, which can become unmanageable and confusing for not only others, but yourself.

At minimum, I suggest the following folder structure for any analysis project:

my_project/
  |
  |- data/
  |
  |- analysis/
  |
  +- output/

I put all my data sets in the data folder, any code I write for analysis in the analysis folder (sometimes I will name this code or src), and finally cleaned data sets or other outputs such as figures in the output folder. You can adapt this general folder structure as you need.

Here is a paper reference that discusses the theory a bit further:

Noble WS. (2009). “A Quick Guide to Organizing Computational Biology Projects.” PLoS Comput Biol 5(7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424