RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data

Autor:	Steffen Heber, Jose M. Alonso, Patrick Perkins, Serina M. Mazzoni-Putman, Anna Stepanova
Jazyk:	angličtina
Rok vydání:	2019
Předmět:	0106 biological sciences Quality Control lcsh:QH426-470 lcsh:Biotechnology Data analysis Biology Web Browser computer.software_genre 01 natural sciences Personalization Bioconductor 03 medical and health sciences Software Ribo-seq lcsh:TP248.13-248.65 Genetics Computer Graphics Web application Humans RNA Messenger 030304 developmental biology 0303 health sciences business.industry Sequence Analysis RNA Research High-Throughput Nucleotide Sequencing Usability Genomics Visualization lcsh:Genetics Protein Biosynthesis Next-generation sequencing Anomaly detection Data pre-processing Data mining business Transcriptome computer Ribosomes 010606 plant biology & botany Biotechnology
Zdroj:	BMC Genomics, Vol 20, Iss S5, Pp 1-9 (2019) BMC Genomics
ISSN:	1471-2164
DOI:	10.1186/s12864-019-5700-7
Popis:	Background Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell’s transcriptome. In practice, Ribo-seq data analysis can be sensitive to quality issues such as read length variation, low read periodicities, and contaminations with ribosomal and transfer RNA. Various software tools for data preprocessing, quality assessment, analysis, and visualization of Ribo-seq data have been developed. However, many of these tools require considerable practical knowledge of software applications, and often multiple different tools have to be used in combination with each other. Results We present riboStreamR, a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application. RiboStreamR provides visualization and analysis tools for various Ribo-seq QC metrics, including read length distribution, read periodicity, and translational efficiency. Our platform is focused on providing a user-friendly experience, and includes various options for graphical customization, report generation, and anomaly detection within Ribo-seq datasets. Conclusions RiboStreamR takes advantage of the vast resources provided by the R and Bioconductor environments, and utilizes the Shiny R package to ensure a high level of usability. Our goal is to develop a tool which facilitates in-depth quality assessment of Ribo-seq data by providing reference datasets and automatically highlighting quality issues and anomalies within datasets. Electronic supplementary material The online version of this article (10.1186/s12864-019-5700-7) contains supplementary material, which is available to authorized users.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf8973498fae944be1fb1ba020a064ad http://link.springer.com/article/10.1186/s12864-019-5700-7 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
Nepřihlášeným uživatelům se plný text nezobrazuje	K zobrazení výsledku je třeba se přihlásit.