abbreviateLabels        Abbreviate lipid labels for lipid module
addHighlyExpressedEdges
                        Add reactions without highly changing genes but
                        with high average expression
collapseAtomsIntoMetabolites
                        Collapse atoms belonging to the same metabolite
                        into one vertex
connectAtomsInsideMetabolite
                        Connect atoms belonging to the same metabolite
                        with edges
createShinyCyJSWidget   Creates shinyCyJS widget from module
gEx                     Example metabolic graph with atom topology.
gatom                   gatom: a package for finding an active
                        metabolic module in atom transition network
gene.de.rawEx           Example gene differential expression data.
getGeneDEMeta           Finds columns in gene differential expression
                        table required for gatom analysis
getMetDEMeta            Finds columns in differential expression table
                        for metabolites required for gatom analysis
getMetabolicPathways    Generate list of metabolic pathways from
                        Reactome and KEGG databases
gsEx                    Example scored metabolic graph with atom
                        topology.
mEx                     Example metabolic module.
makeMetabolicGraph      Creates metabolic graph based on specified data
makeOrgGatomAnnotation
                        Create an organism annotation object for
                        network analysis
met.de.rawEx            Example metabolite differential abundance data.
met.kegg.dbEx           Example KEGG-based metabolite database object
networkEx               Example KEGG-based network object
org.Mm.eg.gatom.annoEx
                        Example organism annotation object
prepareDE               Makes data.table with differential expression
                        results containing all columns required for
                        gatom and in the expected format based on
                        metadata object
saveModuleToDot         Save module to a graphviz dot file
saveModuleToHtml        Save module to a html widget
saveModuleToPdf         Save module to a nice pdf file
saveModuleToXgmml       Save module to an XGMML file
scoreGraph              Score metabolic graph
