Abstract RNA-seq analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of reliance on specialized bioinformatics skills. Thus, we have developed “ 3D RNA-seq ”, an R shiny App and web based service which provides an easy-to-use, flexible and powerful tool for three-component analysis of RNA-seq data: Differential Expression, Differential Alternative Splicing and Differential Transcript Usage. 3D RNA-seq integrates state-of-the-art, highly rated differential expression analysis tools and adopts best practice for RNA-seq analysis. It operates through a user-friendly graphical interface, can handle complex experimental designs, allows setting of statistical parameters, tracks results through graphics and tables, and generates figures and a comprehensive report that will guarantee reproducibility. 3D RNA-seq can be applied to any species and is designed to be run by biologists with no programming skills (or by bioinformaticians) allowing lab scientists to perform rapid and accurate analysis of RNA-seq data.

A powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists