Is it possible to use only the differential expression module of Deseq2 or any other method for miRNA isoforms expression?

I have normalized my data using RPM based normalization and looking to check the differential expression and log fold change. is there any methods so that i can test with more than one statistics to strengthen my analysis.

Thanks in Advance

Yes, I have heard of DESeq2 being used for differential microRNA expression, however, you should use counts instead of normalized expression values. This is discussed in the vignette.