How to ID cell types using reference scRNAseq dataset

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I'm very new to scRNAseq analysis, and I really appreciate any inputs and comments. Your feedback would help me a lot.

I have been given 3 groups data (4 normal, 8 disease and 8 treatment samples), what is the workflow to identify how man cell types and also ID the cell types using reference dataset(mergeomics.research.idre.ucla.edu/PVDSingleCell/CellBrowser/?ds=PAHRatLungs#) in each group?

This question might sounds too general. Specifically, I wonder whether I need to merge data within each group and then perform analysis for each group separately? or I should merge and integrate all 20 samples together? For QC, from my limited understanding, I should perform QC on each samples (20 in total) before doing any computation analysis, right?

Thank you so much for the kindly help!


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