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bioRxiv · 10.1101/2021.01.16.426936

ORFik: a comprehensive R toolkit for the analysis of translation

Tjeldnes, H.·Labun, K.·Torres Cleuren, Y. N.·Chyzynyska, K.·Swirski, M.·Valen, E.
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Abstract

* BackgroundWith the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, analyzing, and characterizing data produced by these assays. * ResultsHere, we introduce ORFik, a user-friendly R/Bioconductor toolbox for studying translation and its regulation. It extends GenomicRanges from the genome to the transcriptome and implements a framework that integrates data from several sources. ORFik streamlines the steps to process, analyze, and visualize the different steps of translation with a particular focus on initiation and elongation. It accepts high-throughput sequencing data from ribosome profiling to quantify ribosome elongation or RCP-seq/TCP-seq to also quantify ribosome scanning. In addition, ORFik can use CAGE data to accurately determine 5UTRs and RNA-seq for determining translation relative to RNA abundance. ORFik supports and calculates over 30 different translation-related features and metrics from the literature and can annotate translated regions such as proteins or upstream open reading frames. As a use-case, we demonstrate using ORFik to rapidly annotate the dynamics of 5 UTRs across different tissues, detect their uORFs, and characterize their scanning and translation in the downstream protein-coding regions. * Availabilityhttp://bioconductor.org/packages/ORFik

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Tjeldnes, H., Labun, K., Torres Cleuren, Y. N., Chyzynyska, K., Swirski, M., Valen, E.. 2021-01-18. ORFik: a comprehensive R toolkit for the analysis of translation. https://doi.org/10.1101/2021.01.16.426936

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