A general workflow for using the RWRtoolkit. (a) Illustration of how a user can generate several network layers from different omics data sources, which become input to the RWRtoolkit workflow. Once the user has networks in the correct format, they can then refer to them via a flist file and use RWR_make_multiplex to turn them into a homogeneous multiplex network (e.g., multiple layers of gene-to-gene relationships). This multiplex is wrapped in an Rdata object that is saved for future use. (b) A demonstration of how the user can now execute a variety of multi-omic analyses, most of which require the Rdata object as input. A set of genes of interest (gene set) from discovery studies such as GWAS or differential expression analysis can be used as input to multiple tools. These tools output a variety of files that show how functionally connected the genes in the gene set are to each other, or to a second gene set of interest, or to all the other genes in the multiplex. Some resulting networks can be automatically visualized in Cytoscape via the RCy3 R package [23]. This figure uses illustrations created with BioRender.com.