scRNA-seq : about the sets of non-differential genes between the clusters of cells

Question

[Bogdan]

Dear all,

would you please let me know :

shall we have a scRNA-seq dataset, with a few clusters - let's say : cluster_A and cluster_B :

if there a (quick) way to get the NON-differential expressed genes between the clusters A and B ?

(in Seurat 2 or Seurat 3, for example, could I set up the FindMarkers() in such a way that it lists also the NON-differential expressed genes between cluster_A and cluster_B ? ).

I'd think that a longer process is to extract all the genes associated with cluster_A, or with cluster_B, and put aside the DEG between clusterA and clusterB .. thank you !

-- bogdan

[Bogdan]

thanks a lot, Igor ! great suggestions !

Answer 1

[igor]

You can run FindMarkers() without a cutoff. By default, logfc.threshold is set to 0.25. You can change that to 0. That will give you all the genes, including those that are not changing. You can then filter the resulting data frame manually as you see fit.