Background: With 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. Results: Here, 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 5'UTRs 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.

中文翻译：

---

ORFik：全面的R工具包，用于翻译分析

背景：随着高通量方法用于表征翻译的需求迅速增长，以及多组学的不断扩展，需要用于处理，分析和表征这些测定所产生数据的后端功能和简化工具。结果：在这里，我们介绍ORFik，这是一种易于使用的R / Bioconductor工具箱，用于研究翻译及其调控。它将GenomicRanges从基因组扩展到转录组，并实现了一个框架，该框架整合了来自多个来源的数据。ORFik简化了处理，分析和可视化翻译不同步骤的步骤，特别着重于起始和延伸。它接受来自核糖体谱分析的高通量测序数据以定量核糖体延伸或RCP-seq / TCP-seq也定量核糖体扫描。此外，ORFik可以使用CAGE数据准确确定5'UTR和RNA-seq，以确定相对于RNA丰度的翻译。ORFik支持和计算来自文献的30多种不同的翻译相关功能和度量，并可以注释翻译区域，例如蛋白质或上游开放阅读框。作为一个用例，我们演示了使用ORFik快速注释不同组织中5'UTR的动力学，检测其uORF并表征其在下游蛋白质编码区域的扫描和翻译。ORFik支持和计算来自文献的30多种不同的翻译相关功能和度量，并可以注释翻译区域，例如蛋白质或上游开放阅读框。作为一个用例，我们演示了使用ORFik快速注释不同组织中5'UTR的动力学，检测其uORF并表征其在下游蛋白质编码区域的扫描和翻译。ORFik支持和计算来自文献的30多种不同的翻译相关功能和度量，并可以注释翻译区域，例如蛋白质或上游开放阅读框。作为一个用例，我们演示了使用ORFik快速注释不同组织中5'UTR的动力学，检测其uORF并表征其在下游蛋白质编码区域的扫描和翻译。