Comfy RStudio IDE

Workbench users

⌨🔥 Exercise: Create a new project and clone the source files we will be using, from GitHub.

If you are using Workbench, start a new session. Then, go to the Menu:

• File -> New project... -> Version Control -> Git

Repository URL: https://github.com/maxplanck-ie/Rseurat
Project directory name: chose a folder name (e.g. MYFOLDER)

• create the project as a subdirectory under one of your group volumes (e.g. /data/PI/group/MYFOLDER), a processing volume (e.g. /data/processing/MYFOLDER), or the scratch space (e.g. /scratch/local/MYFOLDER).

Local users

Go to https://github.com/maxplanck-ie/Rseurat , click on the green < > Code dropdown button and select Download ZIP. Save the file to an appropriate location and extract its content.

Now open your Rstudio IDE, and set the working directory to the folder you have just extracted.

Verification

If it worked, you should have a new session, and in your console you will retrieve your chosen project directory:

getwd()

and you should be able to see the documents:

list.files(‘rmd’)

which should contain subfolders ‘datasets’ and ‘images’, along with a bunch of RMarkdown documents. The latter, is the “raw” content of what you find online at http://maxplanck-ie.github.io/Rseurat.

Our filenames start with two digits (e.g. 14_FirstSteps.Rmd) to set the correct ordering while using alphabetical criteria, e.g. all that’s in the range 10-19 goes into Day #1. The file _site.yml is an index (it defines the “Modules” menu on the website).