Comparison of two populations of scRNAseq cells

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I'm currently analysing an experiment of single cell RNA-seq consisting of two populations of cells both consisting predominantly of the same 3 cell types.
When plotted on a UMAP/tSNE there is a clear separation between the two populations which can mostly be removed via batch correction, however the nature of our experiment means that we would like to identify the differences between the two populations as one is effectively a model of the other. We would thus like to identify the differences between our model population and the wild type population.

I've performed basic analyses such as differential expression between identical cells types across the two populations, however are there any options for further detailed analysis that I might consider?

Thank you.


scRNA-seq


RNA-seq


compare


single-cell

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