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Comrades-OO: An Object-Oriented R Package for Comprehensive Analysis of RNA Structure Generated using RNA crosslinking experiments

ABSTRACT: RNA molecules have secondary and tertiary structures in vivo which play a crucial role in various cellular processes such as the regulation of gene expression, RNA processing, and localization. Investigating these structures will enhance our understanding of their functions 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 complex in vivo RNA structural data. Here, we present COMRADES Object-Oriented (comrades-OO), a novel software package for the comprehensive analysis of data derived from the COMRADES experiment. comrades-OO 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. COMRADES-OO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction.

ORGANISM(S): Homo sapiens

PROVIDER: GSE246412 | GEO | 2023/10/31

REPOSITORIES: GEO

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comrades-OO: An Object-Oriented R Package for Comprehensive Analysis of RNA Structure Generated using RNA crosslinking experiments

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