comradesOO: An Object-Oriented R Package for the Analysis of RNA Structural Data Generated by RNA crosslinking experiments

Abstract

AbstractSummaryRNA (Ribonucleic Acid) molecules have secondary and tertiary structuresin vivowhich play a crucial role in cellular processes such as the regulation of gene expression, RNA processing, and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analysing complexin vivoRNA structural data. Here, we present COMRADES Object-Oriented (comradesOO), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. comradesOO offers a comprehensive pipeline from raw sequencing reads to the identification of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. comradesOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction.Availability and ImplementationcomradesOO is freely available to non-commercial users and implemented in R, with the source code and documentation accessible at [https://CRAN.R-project.org/package=comradesOO]. The software is supported on Linux, macOS, and Windows platforms.Contactjlp76@cam.ac.ukSupplementary informationSupplementary data are available atBioinformaticsonline.