Fig. 1

DA distributions from the same ATAC-seq data set analyzed by 8 different DA approaches. Example MA plots for ATAC-enriched regions of interest analyzed for differential accessibility by different approaches. I and II are from DiffBind using MACS2 peak sets and with scaling factors derived from full libraries or reads in peaks only, respectively. III and IV are from csaw using MACS2 peak sets as query regions with either a TMM or non-linear loess-based normalization method. Likewise, V and VI are from csaw, but instead using de novo query regions identified through local neighborhood enrichment. VII was calculated using MACS2 peak sets transformed to log₂ counts per million (log₂CPM) by voom which is further quantile normalized in VIII. MA plot X-axis represents average ATAC signal abundance at that region, while Y-axis is the log₂ difference in ATAC signal between the two conditions. Black dots represent non-significant regions, and red dots represent significant (FDR < 0.10) DA regions. Blue lines are loess fits to each distribution with 95% confidence intervals shaded in gray