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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

By Michael I Love, Wolfgang Huber, Simon Anders

Posted 19 Feb 2014
bioRxiv DOI: 10.1101/002832 (published DOI: 10.1186/s13059-014-0550-8)

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq data, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data. DESeq2 uses shrinkage estimation for dispersions and fold changes to improve stability and interpretability of the estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression and facilitates downstream tasks such as gene ranking and visualization. DESeq2 is available as an R/Bioconductor package.

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