How to do differential expression analysis on ATAC-SEQ

Hello! My apologies if a stupid question- I have just completed the tutorial on atac-seq analysis for peak calling. I was wondering whether there are any tutorials on how to conduct differential expression between two atac-seq samples? All I’ve seen online is doing it in R- and I was wondering whether its possible to continue to do it in galaxy?
Many thanks in advance!

Hi @mfaleevs

You can use R in Galaxy. Search the training site with the keyword rstudio to find the introduction/orientation tutorial.

Not all tools that have been ported over to Galaxy have a full tutorial of course. What is at the training site are examples of converting command-line methods. That could be applied to any method. To see if the tools (exact, or different that do similar manipulations) are hosted in Galaxy, you can search the tool panel with keywords,. The tool forms have help sections with link-out to author and related resources, including publications with methods. But any published method could probably be converted over.