Reference

Workflow Methods
extract_tables()	Extract tables from a given genome scale metabolic model(GEM) of ".mat" format
signature2gene()	Map metabolic signatures to enzyme-coding genes
enrichment()	Enrichment analysis
hypGEM_to_excel()	Writes the enrichment results out to an Excel workbook
hypGEM_filter()	Filter the enrichment results by fdr value, and optionally sub-selects result columns
refmet_convert()	Convert metabolite names to RefMet via Metabolomics Workbench
Plot Methods
enrichment_plot()	Enrichment analysis visualization
rctbls()	Reactable table for hypeR_GEM_enrichment object
visNet()	Title Query and plot the sub-graph
ggempty()	An empty ggplot
sankey_plot()	Create a 3-layer Sankey diagram (Metabolites → MSETs → GSETs)
Data Objects
Human_GEM_tables	Undirectional mapping tables of Human GEM
Human_GEM_tables_di	Directional mapping tables of Human GEM
Mouse_GEM_tables	Undirectional mapping tables of Mouse GEM
Mouse_GEM_tables_di	Directional mapping tables of Mouse GEM
Rat_GEM_tables	Undirectional mapping tables of Rat GEM
Rat_GEM_tables_di	Directional mapping tables of Rat GEM
Zebrafish_GEM_tables	Undirectional mapping tables of Zebrafish GEM
Zebrafish_GEM_tables_di	Directional mapping tables of Zebrafish GEM
Worm_GEM_tables	Undirectional mapping tables of Worm GEM
Worm_GEM_tables_di	Directional mapping tables of Worm GEM
COVID_serum	Metabolite signatures of COVID obtained from Human serum
COVID_urine	Metabolite signatures of COVID obtained from Human urine
reactome	Reactome genesets
Human_ig	Network of Human GEM
hypeR_object_NECS	Example hypeR-GEM object (NECS)
metabolon_msets_list	Metabolon-based metabolite set list (NECS-derived)
gsets_list	Enriched gene set list (Hallmark, KEGG, Reactome)