Hi,

Can anyone please tell me what are the main differences between Deseq and Deseq2? I guess both work on same statistical test (Negative Binomial distribution).

And for my samples using DESeq package I have used function "nbinomTest" to test for differences between the base means for two conditions. How can I do the same using DESeq2 package. I haven't found any function for this. 

Thank you.

For the differences in methodology (which are substantial), please see our paper. For explanations on how to do a simple two-group comparison, please see the Bioconductor RNA-Seq workflow or the DESeq2 package vignette.