Fig. 8

DCS tool performance and guidelines for DCS tool selection. a Heatmap summarizing DCS tool performance. Columns represent top AUPRC values, accuracy profiles, stability, runtime, memory consumption, and mean DCS score of the benchmarked DCS tools. The AUPRC of the best parameter setup per DCS tool is shown for peak shape and regulation scenarios and their respective combinations. All other metrics are shown as average of all parameter setups per DCS tool over all test scenarios. Standard deviations were calculated between AUPRCs of the simulated and sub-sampled replicates. The number of NA results summarizes all failed and faulty execution runs or runs with empty outputs. Preparation time represents the time to process the input files preceding DCS prediction. Tools were ordered by their mean DCS score over all test sets. b, c Decision trees listing top-performing parameter setups per DCS tool based on DCS score to guide investigators towards the five top-ranking DCS tools and their parameter setups depending on peak shape and regulation scenario. c Decision tree for situations where shape, regulation, or both are unknown. Here, the ranking is based on DCS score of the combined regulation scenarios for TFs, sharp, and broad marks, the combined peak shapes for 50:50 and 100:0 regulation and over all tested scenarios for situations where shape and regulation are unknown. Colored boxes indicate the applied peak caller for the respective parameter setup and if default, default with custom windows, or adjusted parameters should be used. For detailed information on the setups, see Additional file 4: Table S3 and Additional file 6: Table S5