Uses cases for KeyPathwayMineR.
Every use case was divided into four scripts:
_data_prep.R/.Rmd: Data preparation (Download OMICS data and biological network, Diff. Exp. and creation of indicator matrices)
_kpm.R: Execute KPM on biological network and indicator matrices
_pathway_comparison.Rmd: Compare KPM results with pathway comparison plots and visualise with Shiny
_downstream.Rmd: Enrichment analysis of top pathways