I have two distinct scRNA-seq datasets, both generated from a heterogeneous population of cells. One sample has been treated with a drug, the other has not.
My aim is to identify the distinct cellular subtypes present and then to perform differential expression analysis to identify genes that are regulated by the drug treatment. While it is relatively easy to identify and separate out the subpopulations, I am unsure of how to perform the DGE analysis...
The simplest option is to export averaged transcript counts for each individual gene and then use software such a Gfold to identify differentially expressed genes. This is not a particularly elegant solution however and doesn't make use of the range of transcripts counts for a single gene within a given sub population.
So far, all scRNA-seq related software/packages appear focused on exploring transcriptional differences within a sample set rather than between subsets of cells from different samples. Does anyone know of any software/packages (or other approaches) that might help in this regard?