I am trying to find cell markers to distinguish population A and B using single-cell RNA-seq data publicly available. The snag is that these populations where identified in different studies, and the data is available as raw counts (10x) for one study and TPMs (Smart-seq*) for another.
Any suggestion how to integrate these datasets to perform DE downstream?
I was considering using
SCTransform. Any objections?
*I think. It is not clear from the paper's methods but they sequenced the library with 75PE reads.