I have DE miRNAs and i am trying to find target genes and i couldn't find a R package by using reference genome the most of the packages take species from tools that is already online. Could you please help me about it?
You can try miRanda as it requires only the RNA sequences and a genome fasta file.
i think it is not working or i could not find the way , actually i just want to find prediction. i would be appreciate if you could help me about it...
There is a version at conda you can use I guess. https://anaconda.org/bioconda/miranda
Thank you so much, i will definitely try it.