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

Author

Xi Wang, Xiao-Wo Wang, Likun Wang, Zhixing Feng, and Xuegong Zhang

Subjects
Statistics and Probability, Genetics, Base Sequence, Sequence analysis, Sequence Analysis, RNA, Gene Expression Profiling, Molecular Sequence Data, RNA, RNA-Seq, Biology, Biochemistry, DNA sequencing, Computer Science Applications, Computational Mathematics, R package, Differentially expressed genes, Computational Theory and Mathematics, Gene expression, Programming Languages, Molecular Biology, Gene, Algorithms, Software, Oligonucleotide Array Sequence Analysis
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.

Published
2009

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