DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq).
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Differential methylation analysis for BS-seq data under general experimental design.
Park Y, Wu H.
Bioinformatics. 2016 Jan 27. pii: btw026
Wu H, Wang C and Wu Z
“A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.”
Biostat (2013) 14 (2): 232-243. http://dx.doi.org/10.1093/biostatistics/kxs033.