Man pages for ctlab/gatom
Finding an Active Metabolic Module in Atom Transition Network
| abbreviateLabels | Abbreviate lipid labels for lipid module |
| addHighlyExpressedEdges | Add reactions without highly changing genes but with high... |
| collapseAtomsIntoMetabolites | Collapse atoms belonging to the same metabolite into one... |
| 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... |
| gene.de.rawEx | Example gene differential expression data. |
| getGeneDEMeta | Finds columns in gene differential expression table required... |
| getMetabolicPathways | Generate list of metabolic pathways from Reactome and KEGG... |
| getMetDEMeta | Finds columns in differential expression table for... |
| 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... |
| 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 |
| styleWidget | code adopted from... |
