Differential expression analysis of RNA-seq data at single-base resolution

In derfinder, we fit linear models (as specified by equation (3.1) in the main text) at each base in the genome. To do this, we use methods for estimating regularized linear contrasts as implemented in the limma Bioconductor package (Smyth and others 2004, Smyth 2005). We use a customized version of the lmFit function, keeping the default parameters. For the two-group comparison presented in the manuscript, the test statistic s(l) is a moderated t-statistic, which is similar to the ordinary t-statistic obtained from testing whether β2(l) = 0, but the standard error estimate for β2(l) used it its calculation is shrunk toward a prior variance estimate. This framework allows for the borrowing of information across bases, which makes the statistical results more reliable

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