I have 6 single cell RNA seq samples that include treatments with 2 drugs at 2 time points. I have 2 controls (6 and 10 hours), treated with drug A (6 and 10 hours) and treated with drug B (6 and 10 hours). I want to analyze the data using Seurat. I was going to do the QC analysis for each sample, then integrate all the samples and cluster the cells like in the Seurat tutorial. I would like to do differential expression analysis at the end. In the tutorial they seem to be comparing only two groups at a time. Is there a way to compare more than the 2 groups? For example, can I compare the control, drug A and drug B at 6 hours?
Also, I want to do pseudotime analysis so I was planning to use Monocle3. Is this a good tutorial to use (http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/monocle3.html)? The steps seem quite different to the monocle3 documentation.
Are there other packages that people prefer?