Hope you are well. I am a very newbie in single cell RNAseq and I am learning to analyse the data in our lab. I am wondering whether you could explain the purpose of integration in a simple description.
Scenario: Say, we have three experimental groups (three sample per group), Group 1 (control), Group 2 (treatment: Drug A), Group 3 (treatment: Drug C). From what I read and understood, integration means combining cells from each sample together into a single sample of group 1, group 2 and group 3 rather than combining cells from group 1, 2 and 3 together? Kindly help explain!
Can we generate the percentage of cell types from each sample from single cell data, so we can do comparison between group like flow cytometry? or compare gene expression of each cell type between group.. I am looking forward to hearing from you soon.