%0 Journal Article %A Michael I Love %A Wolfgang Huber %A Simon Anders %T Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 %D 2014 %R 10.1101/002832 %J bioRxiv %P 002832 %X In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, 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, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. %U https://www.biorxiv.org/content/biorxiv/early/2014/11/17/002832.full.pdf