Hello Biostars!
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 :)
It's pretty cool. One of the best package I found today. Thank you.
But I am still not fully satisfied, its manual says : 'Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation)'.
Can it be customized for different species too, somehow?
On which species are you working? It can be that the data you require simply does not yet exist.
Right now I'm doing testing on Human data. But I've to work on Danio rerio in few days..
Okay, you may get some ideas from this study:
In additon, this database appears to have zebrafish: