Large-scale RNAseq has substantially changed the transcriptomics field, as it 
enables an unprecedented amount of high resolution data to be acquired. However, 
the analysis of these data still poses a challenge to the research community. 
Many tools have been developed to overcome this problem, and to facilitate the 
study of miRNA expression profiles and those of their target genes. While a few 
of these enable both kinds of analysis to be performed, they also present 
certain limitations in terms of their requirements and/or the restrictions on 
data uploading. To avoid these restraints, we have developed a suite that offers 
the identification of miRNA, mRNA and circRNAs that can be applied to any 
sequenced organism. Additionally, it enables differential expression, miRNA-mRNA 
target prediction and/or functional analysis. The miARma-Seq pipeline is 
presented as a stand-alone tool that is both easy to install and flexible in 
terms of its use, and that brings together well-established software in a single 
bundle. Our suite can analyze a large number of samples due to its multithread 
design. By testing miARma-Seq in validated datasets, we demonstrate here the 
benefits that can be gained from this tool by making it readily accessible to 
the research community.