I have 3 Bulk RNAseq samples from immune cells (Naive, Population1 and Population2), similarly I have two other immune populations from Single Cell RNAseq samples.
I am interested in comparing 3 Bulk RNAseq and 2 single cell RNA seq. Any thoughts, papers and suggestions are welcomed.
I don't know - perhaps define clusters in the scRNA-seq data, get the genes that are highly expressed in these clusters, and then check for the expression of these in the bulk data.
Similar to the above, you could also do a rudimentary de-convolution by defining a signature for each identified scRNA-seq cluster, and then use these in the bulk data in order to infer cell-types [in the bulk data].
What do you mean by "comparing" ?