DSS is an R library for differential expression analysis in RNA-seq count-based data and differential methylation (DML/DMRs) in bisulfite sequencing (BS-seq) data. For the estimation of the dispersion of the count data, the DSS algorithm uses an empirical Bayes shrinkage estimate (Gamma-Poisson or Beta-Binomial distributions). To handle varied sequencing coverages, it uses comparisons between two groups to obtain dispersion shrinkage for multiple factors. For differential expression, it uses the Wald test. DSS fits the Generalized Linear Model (GLM) using edgeR (see links). The DSS algorithm tends to under-estimate the false discovery rate (FDR).
Sequencing; RNA-Seq
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