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Bioinformatics Advance Access published online on October 24, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp612
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Likun Wang 1,2, Zhixing Feng 1, Xi Wang 1, Xiaowo Wang 1,* and Xuegong Zhang 1,*

1MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China.
2College of Computer Science and Technology, Jilin University, Changchun 130012, China.

*To whom correspondence should be addressed. Xiaowo Wang, Xuegong Zhang E-mail: xwwang{at}tsinghua.edu.cn, zhangxg{at}tsinghua.edu.cn


  Abstract

Summary: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference.

Availability: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq

Contact: XW: xwwang{at}tsinghua.edu.cn; XZ: zhangxg{at}tsinghua.edu.cn.

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Ivo Hofacker

Received on July 19, 2009; revised on September 30, 2009; accepted on October 19, 2009

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