Bioinformatics. 2010 Jan 1;26(1):136-8. Epub 2009 Oct 24.

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

Wang L, Feng Z, Wang X, Wang X, Zhang X.

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MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua, University, Beijing 100084, China.

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

PMID:: 19855105; [PubMed - indexed for MEDLINE]

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