We have RNA-seq data from libraries prepared using the Smartseq2 single-cell protocol on 500 cells (mini-bulk) / library. The complexity is much better than with single-cells (~14k genes for 1.5M reads).
6 cell types / biological replicates were collected with flow cytometry, and there are 4 control and 5 diseased biological replicates (patients).
We are mostly interested in the differences between control and disease either overall or within each cell type.
Can single-cell tools (e.g. Seurat) be used on this dataset? It is neither bulk nor single-cell data. How would you approach this?