From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
The University of Melbourne · Walter and Eliza Hall Institute of Medical Research · +3 more institutions
Abstract
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential…
Citation impact
- FWCI
- 15.49
- Percentile
- 100%
- References
- 33
Authors
3- YCYunshun ChenCorresponding
The University of Melbourne, Walter and Eliza Hall Institute of Medical Research
- ATAaron T. L. Lun
University of Cambridge, University of Malaya, Cancer Research UK Cambridge Center
- GKGordon K. Smyth
The University of Melbourne, Walter and Eliza Hall Institute of Medical Research
Topics & keywords
- Bioconductor
- RNA-Seq
- Computational biology
- Workflow
- R package
- Gene expression profiling
- Biology
- RNA
- Industry, innovation and infrastructure