I would recommend that you review the Guided tutorial, Multiple dataset integration (specifically the SCT method), and the Stimulated vs Control PBMCs, in that order. Due the large probable size of your final dataset, I think that the manipulations found within the Mouse Cell Atlas Vignette might also prove useful. The VIsualization and Cell cycle regression vignettes were also particularly helpful for our analysis of similar conditions. Lastly, I recommend that you review the methods in Farnsworth et al. 2020 as well as Soldatov et al., 2019 for further help. Hope that this was useful.

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Thank you for your reply :)

@aubreyghoward Thanks for your help.