Opinions on scMultiome pipeline

[kryptonitecircuit2002]

Hello all!

I am currently analysing single cell multiome data and the data has been generated across two conditions: control and knockdown. Essentially, I want to compare how the genomic and epigenomic changes alter the cellular landscape across the conditions. I looked up vignettes, trouble shot things and finally this is the code I have:

https://github.com/kryptonitecircuit2002/scMultiome/blob/1d6d3d9b3a0cb6a8e91ae0fbf2e5859a0024219e/Main%20Script_Sublime.R

Since this is my first time doing this, opinions from experts is highly valuable to me. Do let me know of any mistakes or discrepancies you might see. So far, it has worked fine, except for LinkPeaks function, which does not seem to run. Please give your opinions on whether I need to modify or change anything, or add anything to my script to make it more accurate.