Man pages for ctlab/gatom
Finding an Active Metabolic Module in Atom Transition Network

abbreviateLabelsAbbreviate lipid labels for lipid module
addHighlyExpressedEdgesAdd reactions without highly changing genes but with high...
collapseAtomsIntoMetabolitesCollapse atoms belonging to the same metabolite into one...
connectAtomsInsideMetaboliteConnect atoms belonging to the same metabolite with edges
createShinyCyJSWidgetCreates shinyCyJS widget from module
gatomgatom: a package for finding an active metabolic module in...
gene.de.rawExExample gene differential expression data.
getGeneDEMetaFinds columns in gene differential expression table required...
getMetabolicPathwaysGenerate list of metabolic pathways from Reactome and KEGG...
getMetDEMetaFinds columns in differential expression table for...
gExExample metabolic graph with atom topology.
gsExExample scored metabolic graph with atom topology.
makeMetabolicGraphCreates metabolic graph based on specified data
makeOrgGatomAnnotationCreate an organism annotation object for network analysis
met.de.rawExExample metabolite differential abundance data.
met.kegg.dbExExample KEGG-based metabolite database object
mExExample metabolic module.
networkExExample KEGG-based network object
org.Mm.eg.gatom.annoExExample organism annotation object
prepareDEMakes data.table with differential expression results...
saveModuleToDotSave module to a graphviz dot file
saveModuleToHtmlSave module to a html widget
saveModuleToPdfSave module to a nice pdf file
saveModuleToXgmmlSave module to an XGMML file
scoreGraphScore metabolic graph
styleWidgetcode adopted from...
ctlab/gatom documentation built on May 3, 2024, 3:44 p.m.