mixOmics is one of the best tools for multi-omics analysis. Before using Diablo multi-omics, I would recommend doing some ground work with the sparse Partial Least Squares Discriminant Analysis (sPLS-DA) tool in each *-omics domain.
You do not have to go in with a list of genes/proteins/biologics/etc (variables) of interest. In a typical setup, one selects variables in each *-omics domain based on entropy (this is referred to as variable importance, vip). One has to formulate a meaningful contrast though, e.g. neurotypical vs. PD or multiple hypothesized PD sub-types, and with regards to that, mixOmics sets up a predictor and computes the its performance, expressed as the balanced error rate (BER).
The online case studies are very useful and the tool copes well with (sparse) microbiome data.