Please use this identifier to cite or link to this item:
http://doi.org/10.25358/openscience-5739
Authors: | Marini, Federico Linke, Jan Binder, Harald |
Title: | ideal: an R/Bioconductor package for interactive diferential expression analysis |
Online publication date: | 21-Apr-2021 |
Year of first publication: | 2020 |
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 (http://bioconductor.org/packages/ideal/), 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 |
ROR: | https://ror.org/023b0x485 |
DOI: | http://doi.org/10.25358/openscience-5739 |
Version: | Published version |
Publication type: | Zeitschriftenaufsatz |
License: | CC BY |
Information on rights of use: | https://creativecommons.org/licenses/by/4.0/ |
Journal: | BMC bioinformatics 21 |
Pages or article number: | 565 |
Publisher: | BioMed Central |
Publisher place: | London |
Issue date: | 2020 |
ISSN: | 1471-2105 |
Publisher URL: | https://doi.org/10.1186/s12859-020-03819-5 |
Publisher DOI: | 10.1186/s12859-020-03819-5 |
Appears in collections: | JGU-Publikationen |
Files in This Item:
File | Description | Size | Format | ||
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marini_federico-ideal__an_r/bi-20210414122937882.pdf | 1.42 MB | Adobe PDF | View/Open |