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

Abstract

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.

Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures

“…The methodology and results specified in this study provide an insight into the systematic analysis of LC-MS data analysis and elaborate on the use of computational processing using R. 42 R plays a significant role in cheminformatics and mass spectrometry via manipulating and analyzing chemical structures and data within the R environment. Many cheminformatics packages are available including rcdk, MSnbase, RMassBank and RChemMass, with several more packages available through CRAN, 43 BioConductor and GitHub. Integrating the above packages into the R environment facilitates the development of new strategies in data handling, manipulation and implementation of a graphical user interface to serve as a platform for analyzing LC-MS data, preprocessing and visualization.…”

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

“…riboviz 2 can be used on any organism for which a transcriptome FASTA and GFF3 file can be constructed, making it a valuable tool for users studying either model or non-model organisms. This is an advantage for riboviz 2 compared to other GUI or command-line based tools that are limited to a set of organisms or require sequence annotations to be downloaded from a specific database ( Liu et al , 2020 ; Perkins et al , 2019 ; Verbruggen et al , 2019 ; Wang et al , 2018 ). The user is responsible for supplying a FASTA file appropriate to their biological question, e.g.…”

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

“…Instead, a more detailed comparison was made to other online databases which either provide pre-processed data or provide an easy way to process Ribo-Seq data which does not require computational expertise. These tools include RiboToolKit ( 7 ), SmProt ( 45 ), HRPDViewer ( 46 ), TranslatomeDB ( 15 ), RiboViz ( 47 ), RPFdb ( 12 ), OpenProt ( 13 ), GWIPS-Viz ( 48 ), RiboGalaxy ( 6 ) and RiboStreamR ( 49 ). The features of these tools are listed in Table 1 .…”