Fig. 1

Schematic illustration of the high-throughput structural (HTS) analytical process and reactIDR. a Major types of HTS-associated experimental designs analyzed in this study. All experimental approaches can be classified into the listed groups, according to the number of sample conditions and their detection targets. Red and blue stars represent a probing occurrence at the loop and stem regions, respectively. b Applicability of the reactivity-scoring methods to three types of HTS experimental designs (i.e., whether the method is intended to analyze each type of experiment or not), in which Score indicates each threshold-based scoring method used for studying the icSHAPE and PARS analyses. c Overview of reactIDR procedures. reactIDR receives the input data consisting of 5^′-end read-depths repeatedly measured in a single or two conditions. The input data, after trimming of the very ends of the transcripts, is converted into the scaled ranking data to adapt the copula model. Afterward, a posterior loop probability distribution at each site can be computed as an index of reactivity