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rnaCrosslinkOO: An Object-Oriented R Package for the Analysis of RNA Structural Data Generated by RNA Crosslinking Experiments.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Price, Jonathan L 
Ziv, Omer 
Pinckert, Malte L 
Lim, Andrew 
Miska, Eric A 

Abstract

SUMMARY: RNA (Ribonucleic Acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localisation. 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 complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction. AVAILABILITY AND IMPLEMENTATION: rnaCrosslinkOO 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=rnaCrosslinkOO]. The software is supported on Linux, macOS, and Windows platforms.

Description

Keywords

31 Biological Sciences, 3102 Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics

Journal Title

Bioinformatics

Conference Name

Journal ISSN

1367-4803
1367-4811

Volume Title

Publisher

Oxford University Press (OUP)
Sponsorship
Wellcome Trust (104640/Z/14/Z)