I have an RNAseq data of a human cell line, with three experimental conditions(having 3 replicates each). The depth of all the samples is >80M. The same samples were also sequenced for small RNA(miRNAs), with help of some miRNA target prediction algorithms and databases I was able to predict some sponge circuits in my RNASeq data.
Similarly, I was hoping to find some information on interactions between these protein and lncRNAs in the sponge circuits. Are there any recently updated databases or R packages available to perform such analysis? Or any machine learning algorithms?
Some validation on these sponge circuits might help me to solidify my results.
Thank you in advance.