I'm quite confused what's the workflow after I get the output from singleR output. I have 3 groups scRNAseq data(4 control, 8 treatment1, 8 treatment2), and my goal is to give cell type annotation for each group. And now, I just learned how to perform QC, normalization, dimension reduction, and singleR for one dataset. To give the cell type for each group, should I integrate datasets within each group separately, and then using singleR? specifically, how to assign the cell type to each cluster on my tSNE plot for each group?
I really appreciate any comment, thank you.