Fig. 1

MPRAnalyze model properties and fit. a Distribution of construct abundances (DNA barcodes) across datasets, computed as the observed barcode count + 1 for visualization purposes. b A graphical representation of the MPRAnalyze model. External covariates (e.g., conditions of interest, batch effects, barcode effects) are design-dependent. Latent construct and transcript counts are related by the transcription rate α. c Goodness of fit plots for both DNA and RNA libraries across datasets. Expected counts were extracted from the fitted GLMs. MPRAnalyze’s model fits MPRA data well, with R²>0.86 across all datasets. Since the Kwasnieski data only has one replicate in the DNA library, the DNA model is able to reach a perfect fit, in which case the DNA estimates used in the RNA model are identical to the original DNA counts