i have two scRNA-seq datasets (replicate 1, replicate 2).
I would like to compare how many genes were detected, average expression of genes, in brief: an estimate of how similar (reproducible) the replicates are, in terms of how well they correlate. Any hints, ideas, points where i would find code snippets of what is the best approach to this? (I am learning Seurat but happy to check out other software, like Scanpy)
Currently i am trying to normalize the data and plot average gene expression rep1 vs rep2.
Thanks for any help, Gregor