Single-cell preprocessing with Seurat

[Ivo Kwee]

[Originally emailed by KT on 13.08.2020]

I'm going to work on a script for processing Seurat and/or anndata files into .pgx files, though if you're already doing that, please let me know!

[Ivo Kwee]

Please look at some of the scRNA-seq scripts in the .../scripts folder, e.g. that for the melanoma data set. These times we are processing more and more scRNA-seq data sets from the 10X, so we will have scripts targeting the output of Cell Ranger to pgx. One of the problems is that the Playground gets pretty slow if the number of cells exceed like 1500-2000 cells and more than 10'000 genes. Even with pre-computation. It's just that the plotting will take too long. Our solution will be to pool similar cells and sum up their counts, so it can reduce 30'000 cells to say 1000 cells. I will upload these scripts soon to the repository, but if you are interested I could send an example to you now.