RT Journal Article
SR Electronic
T1 3D RNA-seq - a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 656686
DO 10.1101/656686
A1 Wenbin Guo
A1 Nikoleta Tzioutziou
A1 Gordon Stephen
A1 Iain Milne
A1 Cristiane Calixto
A1 Robbie Waugh
A1 John W. S. Brown
A1 Runxuan Zhang
YR 2019
UL http://biorxiv.org/content/early/2019/05/31/656686.abstract
AB RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on skilled bioinformaticians to perform the analysis. To overcome these issues, we have developed the “3D RNA-seq” App, an R shiny App which provides an easy-to-use, flexible and powerful tool for the three-way differential analysis: Differential Expression (DE), Differential Alternative Splicing (DAS) and Differential Transcript Usage (DTU) of RNA-seq data. The full analysis is extremely rapidand can be done within hours. The program integrates Limma, a state-of-the-art, highly rated differential expression analysis tool and adopts best practice for RNA-seq analysis. It runs the analysis through a user-friendly graphical interface, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of Arabidopsis and mouse RNA-seq data. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to take control of the analysis of their RNA-seq data.