IDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.

ABSTRACT:

Background

RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis.

Results

iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and

SUBMITTER: Ge SX 

PROVIDER: S-EPMC6299935 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature