Normalize scRNAseq data to housekeeping genes to compare several datasets

Question

[AaronJaime]

Hello everyone!

I am aiming to compare some single-cell RNAseq datasets, specifically cell stress level between them. Considering cell type diversity in the tissue, I was thinking on experimental design as normalizing each dataset to housekeeping genes and then statistical comparison.

The thing is I've never done this kind of normalization before and I am relatively new in processing single cell data. So if anybody have a clue about how to handle this issue I would be very grateful.

[ATpoint]

I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.