Note: if you'd like to use this in a Rstudio project template, I've created one here: https://github.com/scottdaniel/basicRstudioTemplate
The most basic bioinformatics R markdown template.
This project was created by following this guide from the friendly folks at Rstudio Inc.
Uses the setup paradigm of "mother" and "child" reports as detailed in this blog post
if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github(repo = "scottdaniel/basicTemplate")
Once installed, you can create a new R markdown file from within Rstudio, just go to New File... > R markdown... > From Template and then select your template as the option and click [OK]
I selected my most commonly used packages as well as some "common_functions" that I used often in my reports. To customize this, just fork the repo, create a new project inside the directory, and then modify the files inside /inst/rmarkdown/templates/boilerplate/skeleton.
After you're done, just Install and Restart under the Build tab. Of course, if you find any bugs / add new features / embetter the code; feel free to create a pull request :)
Rstudio project template that uses this Rmarkdown template