miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
...It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow.
As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together well-established software in a single bundle, allowing a complete analysis from raw data. All the capabilities can be easily and simultaneously enabled at will, regardless the step in the workflow.