Today I'm trying a new pipeline for miRNA prediction. I used 'miRDeep' for miRNA prediction & after that I used 'DESeq' for differential analysis. Now I'm wondering how to get target genes for these miRNA. There're several packages such as targetscan.Hs.eg.db, multiMiR, miRNATarget etc. Which one do you all suggest?
And what all downstream analysis can be done related to miRNA ?
Please do suggest. Thanks you all :)