Applying limma-trend, voom, and DESeq2 to raw read counts

For limma-trend, we first derived log₂-CPM values by using the calcNormFactors and cpm functions of the edgeR package, with log = TRUE for the latter. Then, the standard pipeline of limma was applied to the log₂-CPM values, with trend = TRUE for the eBayes function. For the voom method, the calcNormFactors and voom functions were sequentially called, and the standard limma pipeline was then applied to the returned object. DESeq2 was applied with its standard pipeline as recommended in the documentation.