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Measure transcriptomic cell similarities between experimental groups in Single-cell RNAseq

Hello!

I am working on a project where we have scRNA-seq data from organoids from 3 different experimental conditions (Control, condition A and condition B). We want to measure the "similarity" at a transcriptomic level between control cells vs both conditions cells and study what condition is more similar to the control cells.

Thanks in advance

sc-ruzafa

single-cell sc-rna similarities
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updated by Trivas • Trivas • written by sc-ruzafa • sc-ruzafa

1 answer

My guess is you would cluster your cells by cell type then make a correlation matrix of gene counts within each cell type comparing condition A to your control.

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written by Trivas • Trivas

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