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 |
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 |
getMetabolicPathways | Generate list of metabolic pathways from Reactome and KEGG databases |
getMetDEMeta | Finds columns in differential expression table for metabolites required for gatom analysis |
gEx | Example metabolic graph with atom topology. |
gsEx | Example scored metabolic graph with atom topology. |
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 |
mEx | Example metabolic module. |
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 |