Specifying package dependency in a bioinformatics project (not an R package)


I develop a bioinformatics project in rstudio, which consists of some drivers script to generate data and rmd files for summarizing results. When someone check out my project to reproduce my analyses. I want them to be able to install all the package the project depends on easily.

Do I specify dependencies as if it's a "package" using DESCRIPTION.txt (http://r-pkgs.had.co.nz/description.html#dependencies)

Or is there another way to do this?


There's no standard way to do this outside of a package. I suggest making a README.md file which describes

  • What the project is
  • Required packages
  • Other required software, if any
  • How to run the analysis

As a bonus, these types of files are incredibly useful when revisiting older projects. I make them even for projects I never expect to share.


Thank you for the suggestion. I also thought about using putting it in a docker container but I think a README.md will do for now.


You might also look at Packrat, it might be heavier than what you want but it will help with your package dependency worries.

Not my answer but this might be a good reference for you: