ideal: an R/Bioconductor package for Interactive Differential Expression Analysis

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.

Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier

“…To highlight the differences of the expression values between the two groups, MA-Plots were generated with the R programming language. Further analyses included Gene Ontology pathway enrichment of DEG using topGO [5] (v2.34.0) and goseq (v1.34.0) [86] (with all expressed genes set as background) were performed using the ideal package (version 1.6.0) [52].…”

Bacterial polyphosphates interfere with the innate host defense to infection

“…Exploratory data analysis was performed with the pcaExplorer package (v2.2.1)58 . Differential expression analysis was performed with the ideal package (v1.0.0)59 . DEGs were considered significant if p-adj (adjusted p value) < 0.05 from DESeq2 (v1.16.0).…”

TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation

“…While text-based tutorials and walk-through documents (also in video format) can work efficiently for a specific snapshot of the application, it is not a convenient approach for maintenance once new features are added. Moreover, an approach that encourages the users to try out specific actions tightly linked to defined elements in the user interface has proven useful for other applications such as ideal ( 91 ) and iSEE ( 92 ), offering a learning-by-doing paradigm for showcasing the application features in a more cohesive, workflow-like way.…”