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Authors: Marini, Federico
Linke, Jan
Binder, Harald
Title: ideal: an R/Bioconductor package for interactive diferential expression analysis
Online publication date: 21-Apr-2021
Language: english
Abstract: BACKGROUND RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking. RESULTS We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility. CONCLUSION ideal is distributed as an R package in the Bioconductor project (, and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.
DDC: 610 Medizin
610 Medical sciences
Institution: Johannes Gutenberg-Universität Mainz
Department: FB 04 Medizin
Place: Mainz
Version: Published version
Publication type: Zeitschriftenaufsatz
License: CC BY
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Journal: BMC bioinformatics
Pages or article number: 565
Publisher: BioMed Central
Publisher place: London
Issue date: 2020
ISSN: 1471-2105
Publisher URL:
Publisher DOI: 10.1186/s12859-020-03819-5
Appears in collections:JGU-Publikationen

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