yes you can. Note this is more of a main Bioc mailing list question.

On Fri, Jul 11, 2014 at 3:56 AM, jarod...@libero.it <jarod...@libero.it> wrote:
> Dear All!!
> Can I use Deseq2 for microRNAseq data?
>
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> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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