Gaining insights from RNA-Seq data using iDEP

Abstract

The analysis and interpretation of the RNA-Seq data can be time-consuming and challenging. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly web application for exploratory data analysis, differential expression, and pathway analysis. iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 208 annotation databases for plant and animal species, and 2 web services. The workflow can be reproduced by downloading customized R code and related files. As demonstrated by two examples, iDEP (http://ge-lab.org/idep/) democratizes access to bioinformatics resources and empowers biologists to easily gain actionable insights from transcriptomic data.