RNA in situ conformation sequencing (RIC-seq) is an assay that probes the conformation and structure of RNA using proximity ligation principle. In this assay, RNA molecules are cross-linked through RNA-binding proteins (RBPs) in vivo, which allows the identification of contacts that occur within physiological RNA–RBP complexes and exist in relevant biological contexts. Here, we describe two bioinformatic pipelines: one that extracts RNA contacts from RIC-seq data (RNAcontacts) and the other that uses the obtained information on RNA contacts to predict stable complementary elements of the RNA structure (PHRIC). The former can be used as a standalone tool to discover RNA–RNA interactions in cis and in trans, while the latter can be viewed as its extension, which searches for pairs of nested contact clusters and predicts complementary interactions between them. Both pipelines are implemented in Snakemake, a reproducible and scalable workflow management system for rapid and uniform processing of multiple transcriptomic datasets.