Hi there, I am trying to run combat with 200,000 obs and it is taking 300gb of ram and additional 900 swap file. It is running as serial instead of parallel execution -taking too long to finish and crashes. Is there another tool for batch effect correction that is more efficient in run time and uses all cores?
Thank you
I guess you’ve heard about MNN, CCA, scVI, BBKNN, and others? It all depends on what you want to you the data for: just the embedding, or downstream applications like DE as well. There’s been more than one benchmark, like this.
yea BBKNN worked great for my use case, thanks!