Version 5.0

• SC-ION is now an installable R package (devtools::install_github()), replacing the old download-the-files-and-run-START_SCION.R workflow.
• The Shiny app has been rebuilt as a 3-tab workflow -- Run, Network Diagnostics, Visualize -- plus a Help tab documenting every parameter.
• Added permutation-based FDR thresholding (run_scion(permute = TRUE), permute_network(), compute_fdr_threshold()), with an interactive FDR curve and adjustable cutoff in the app.
• Added network visualization (plot_network()), both a static plot and an interactive one in the app; Cytoscape import is still available for large networks or publication figures.
• Target/regulator/clustering matrices and gene lists now accept CSV, TSV, plain-text, or SSV (in addition to GCT), detected from the file extension -- not just CSV.
• Legacy tutorial and test-data files moved to a legacy/ folder; the SC-ION v3.2 vignette is kept for reference but is historical.