This folder contains three fully reproducible examples of use cases using expressive power and flexibility of the RGMQL package in biologically relevant applications. Open the RProject file [EXAMPLES.Rproj](EXAMPLES.Rproj) to set automatically the working directory for the use cases. For each use case, the complete workflow is available as a R Notebook: also, a corresponding HTML file is available to show the results we previously obtained. We suggest to try also the examples in [vignettes/RGMQL-vignette.Rmd](./../vignettes/RGMQL-vignette.Rmd) to become more familiar with the RGMQL functions, before replicating these workflows.