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

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: xwwang@tsinghua.edu.cn; zhangxg@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

• NN
  National Natural Science Foundation of China

  Awards: 60905013, 60721003
• SU
  Southeast University
• SK
  State Key Laboratory of Bioelectronics
• NK
  National Key Research and Development Program of China

  Awards: 2004CB518605, 60721003
• OR
  Open Research Fund of State Key Laboratory of Bioelectronics