RNA–RNA interactions play a crucial role in cellular processes by regulating gene expression, RNA stability, and posttranscriptional modifications. These interactions have emerged as key players in the intricate network of RNA-based regulatory mechanisms. In recent years, Direct Duplex Detection methods have been widely used to map these interactions on a large scale but require sophisticated data analysis. We describe the analysis of these DDD data using RNAnue to determine RNA–RNA interactions. RNAnue is available at https://github.com/Ibvt/RNAnue .