DOI: 10.1093/bioinformatics/btp612 ISSN:
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
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.