Next generation sequencing technologies, such as RNA-Seq, generate tens of millions of reads to define the expression levels of the features of interest. A wide number and variety of software packages have been developed for accommodating the needs of the researcher, mostly in the R/Bioconductor framework. Many of them focus on the identification of differentially expressed (DE) genes (**DESeq2**, **edgeR**, [@Love2015]) to discover quantitative changes between experimental groups, while other address alternative splicing, discovery of novel transcripts, or RNA editing.
Moreover, Exploratory Data Analysis is a common step to all these workflows, and despite its importance for generating highly reliable results, it is often neglected, as many of the steps involved might require a considerable proficiency of the user in the programming languages. Principal Components Analysis (PCA) is used often to obtain a dimension-reduced overview of the data [@Jolliffe2002].
Our proposal will address the two steps of Exploratory Data Analysis and Differential Expression analysis with two different packages, integrated and available in Bioconductor, namely **pcaExplorer** and **ideal**. We propose web applications developed in the Shiny framework which will also include support for reproducible analyses, thanks to an embedded text editor and a template document, to seamlessly generate HTML reports as a result of the user's exploration.
This solution, which we also outlined in [@Marini2016], serves as a concrete proof of principle of integrating the essential features of interactivity (as a proxy for accessibility) and reproducibility in the same tool, fitting both the needs of life scientists and experienced analyists, thus making our packages good candidates to become companion tools for each RNA-Seq analysis.
