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tracecakes 10-22-2019 10:05 PM

single cell RNA seq - cell abundance per cluster
Hi all :)

I have a simple question but cannot find an answer (maybe I am using the wrong search terms?)

We have single cell RNA seq data (10X Genomics) and are interested in cell types present per sample (case and control).

I have performed all the pre-processing steps with Cell Ranger and Seurat, have obtained clusters per sample, identified cell types using known markers and would now like to compare if one sample has significantly more cells of one cell type than another. What statistical test is appropriate (is it just a chi-squared test?)? Or is it not even appropriate to do a statistical test at, as I only have 2 cases and 2 control samples?

If you have an example in R or even an article that you can link me to that would be really helpful, haven't found one yet and this is new to me.

Many thanks.

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