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

Patrick Perkins1, Serina Mazzoni-Putman2, Anna Stepanova2

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|June 7, 2019
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Summary
This summary is machine-generated.

We developed riboStreamR, a user-friendly R Shiny web application for Ribo-seq quality control. This platform simplifies the assessment of Ribo-seq data quality, identifying potential issues for researchers.

Keywords:
Data analysisNext-generation sequencingRibo-seqWeb application

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Ribo-seq is crucial for studying translation and its regulation.
  • Ribo-seq data analysis faces challenges with quality control, including read length variation and contamination.
  • Existing tools often require extensive expertise and integration.

Purpose of the Study:

  • To present riboStreamR, a comprehensive Ribo-seq quality control (QC) platform.
  • To provide a user-friendly R Shiny web application for Ribo-seq data analysis.
  • To facilitate in-depth quality assessment and anomaly detection in Ribo-seq datasets.

Main Methods:

  • Developed riboStreamR as an R Shiny web application.
  • Integrated visualization and analysis tools for key Ribo-seq QC metrics.
  • Incorporated options for graphical customization, report generation, and anomaly detection.

Main Results:

  • riboStreamR offers visualization for read length distribution, read periodicity, and translational efficiency.
  • The platform provides a user-friendly interface for Ribo-seq data quality assessment.
  • Anomaly detection features highlight potential quality issues within datasets.

Conclusions:

  • riboStreamR leverages R and Bioconductor for high usability via the Shiny R package.
  • The tool aims to simplify Ribo-seq data quality assessment for researchers.
  • It provides reference datasets and automatic highlighting of quality anomalies.