genie3 for lncRNAs and mRNAs co-expression

Question

[Sam]

Dear All

I'm going to use genie3 package for lncRNAs and mRNAs co-expression analysis, can I input just DE mRNAs and DE lncRNAs in this package to differential co-expression analysis?

Thanks

[Biologist]

Instead of using only DE lncRNAs and DE mRNAs, you should input all the mRNAs and lncRNAs with some filtering like removing genes with low expression.

You can check the WGCNA R package for Co-expression network analysis.