I have only two samples. one is Control and other is Treatment. which package can be used for differential analysis between only two samples? No replicates.

How can I do that?

Thank you

We don't recommend to perform these analyses in DESeq2. As far as DESeq2 methods, you could compute the vst() on the counts and then look at differences between the normalized, transformed data, but there's not much point in performing an analysis that computes p-values without replicates.

As Mike has said, there's not much you can do. See Section 2.11 of the edgeR user's guide for details.