I have some miRNA-seq raw data and I need to search for miRNA:mRNA interaction networks. After doing a quick literature review, I found several tools including mirDeep2, mirArma-seq, and other tools. However, I'm still confused about which workflow to use. So, I'd like to consult about this issue and find an appropriate pipeline consisting of open source tools. I'm good at coding in R and Python and also have enough experience using the shell. I don't like to use any GUI tool. I would prefer to stay in the R environment for the post-alignment steps as much as possible. My current bulk RNA-seq workflow is FASTQC-TRIMMOMATIC-KALLISTO-EDGER-LIMMA, so If your recommended pipeline uses these tools, its learning curve would be smoother for me and easier to use.