Gene correlation with single cell data?

Gene correlation with single cell data?


I am a bioinformatician at a research institute and I frequently get requests to perform gene correlations in single cell data. For example: “we would like to correlate the expression of IP6K3 with genes involved in glutamie metabolism in endothelial cells.” Insofar as I was aware, performing correlation such as Pearson or Spearman doesn’t work on single data because of the high numbers of dropouts. This isn’t a problem for bulk RNAseq data, where dropouts are no longer a problem, but you lose resolution in terms of cell type.

Does anyone have any recommendations for tools/packages or statistical approaches to perform gene correlation for single cell data?




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