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

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 su...

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Autores principales: Perkins, Patrick, Mazzoni-Putman, Serina, Stepanova, Anna, Alonso, Jose, Heber, Steffen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551240/
https://www.ncbi.nlm.nih.gov/pubmed/31167636
http://dx.doi.org/10.1186/s12864-019-5700-7
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author Perkins, Patrick
Mazzoni-Putman, Serina
Stepanova, Anna
Alonso, Jose
Heber, Steffen
author_facet Perkins, Patrick
Mazzoni-Putman, Serina
Stepanova, Anna
Alonso, Jose
Heber, Steffen
author_sort Perkins, Patrick
collection PubMed
description 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.
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spelling pubmed-65512402019-06-07 RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data Perkins, Patrick Mazzoni-Putman, Serina Stepanova, Anna Alonso, Jose Heber, Steffen BMC Genomics Research 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. BioMed Central 2019-06-06 /pmc/articles/PMC6551240/ /pubmed/31167636 http://dx.doi.org/10.1186/s12864-019-5700-7 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Perkins, Patrick
Mazzoni-Putman, Serina
Stepanova, Anna
Alonso, Jose
Heber, Steffen
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title_full RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title_fullStr RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title_full_unstemmed RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title_short RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
title_sort ribostreamr: a web application for quality control, analysis, and visualization of ribo-seq data
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551240/
https://www.ncbi.nlm.nih.gov/pubmed/31167636
http://dx.doi.org/10.1186/s12864-019-5700-7
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