Example workfow for analysing gene expression changes in macrophage activation | Starting application | Preparing the dataset for analysis | Exploring the dataset | Differential gene expression | Advanced usage | Gene identifiers conversion with AnnotationDB | Pathway analysis with Enrichr | Metabolic network analysis with Shiny GAM | GSEA enrichment plot | Link sharing | Loading dataset options | Serving Phantasus | Options for servePhantasus | Preloaded datasets | Support for RNA-seq datasets | Pathway database for FGSEA | Annotation database for AnnotationDB tool | Feedback | Acknowledgments | Citation

Installation | Quick start | Supported problem types | Simple MWCS | Budget MWCS | Generalized MWCS (GMWCS) | Signal generalized MWCS (SGMWCS) | Constructing SGMWCS instances | Supported solvers | Rmwcs solver | Rnc solver | Simulated annealing solver | Java-based Virgo solver | SCIP-jack solver | Integration with BioNet

Installation | Example workfow | Saving modules | Example on full data and full network | Networks | KEGG | Rhea | Combined network | Rhea lipid subnetwork | Misc | Supplementary gene files | Non-enzymatic reactions | Using exact solver | Running with no metabolite data | Running with no gene data | Using metabolite-level network | Pathway annotation