the mpra package seems promising to perform differential analysis of massively-parallel reporter assays between conditions, be it genotypes/alleles, tissues or treatments. The comparison takes RNA and DNA counts for both conditions into account and tests for significant differences. So far so good, but how about the identification of significant reporter activity with this framework? Given that I have a DNA library, consisting of 100k genomic elements/regions, which I transfect into cells in several replicates, eventually obtaining counts for RNA and DNA: Can I use this framework to test whether RNA counts are significantly enriched or depleted over DNA counts, distinguishing elements with enhancing or silencing reporter activity from silent elements? If so, could you please recommend a design matrix for this setting?