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TinclG / PAS_analysis

Placenta Accreta Spectrum (PAS) disorders fall within the group of Placental Implantation Abnormalities. In this project we analysed differences in gene expression in the microenvironments of PAS and normal pregnancies.
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Reorganize repo structure #5

Open vjmarteau opened 2 years ago

vjmarteau commented 2 years ago

It would be nice to create some folders to tidy up the repository. I would suggest:

  1. Put notebooks into "analysis" folder
  2. Put functions into "lib" folder
  3. Create an additional "data" folder on your local pc and list it in the .gitignore (to prevent data from being uploaded to GitHub)
  4. Create a "results" folder for figures/etc.
  5. (optional) Create an "envs" folder for yaml files to build an environment for example using Conda.
  6. If you work in RStudio you might want to create a project file (.Rproj) in your main project directory + put into .gitignore file. (Is going to make your life a bit easier)
vjmarteau commented 2 years ago

In general you should try to use R scripts for code and Notebooks to display and comment on data/figures/etc. If you set a structure such as above the different code blocks would go into the "lib" folder and be called as functions into the analysis notebooks. The code itself should mostly be self-explanatory and comments try to answer the "why" rather than "how"

TinclG commented 2 years ago

I put PAS_analysis.Rproj into the gitignore, but it's still shown in the github repo... Also, I tried to make a raw_data folder and put it in gitignore. It was also still shown. Do you have any experiences with putting the whole folder under ignore?

vjmarteau commented 2 years ago

This should work. However since you already pushed the .Rproj file to your repo you will need to delete it on your GitHub repo.

*.Rproj
raw_data/