The BioC package DESeq provides a powerful tool to estimate the variance in count data and test for differential expression. It can estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Variance estimation The core assumption of this method is that the mean is a good predictor of the variance, i.e., that genes with a similar expression level also have similar variance across replicates. Hence, we need to estimate for each condition a function that allows to predict the variance from the mean. This estimation is done by calculating, for each gene, the sample mean and variance within replicates and then tting a curve to this data.