Man pages for tmod
Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

EgambiaGene expression in TB patients and Healthy controls
eigengeneCalculate the eigengene of a module from a data set
evidencePlotCreate an evidence plot for a module
extract-methodsShows the tmod object
getGenesGet genes belonging to a module
getModuleMembersReturn the contents of a module
hgEnrichmentPlotCreate a visualisation of enrichment
lengthShows the length of a tmod object
mbindBind two or more transcriptional module sets
modcorsModule correlation
modjaccardJaccard index for modules
modmetaboModules for metabolic profiling
mtx2msetConvert between matrix representation of modules and tmod...
pcaplotPlot a PCA object returned by prcomp
pvalEffectPlotCreate an effect size / p-value plot
renameModsRename module IDs
showGeneA combined beeswarm / boxplot
showModuleSelect genes belonging to a module from a data frame
simplePieSimple Pie Chart
tmodAUCCalculate AUC
tmod-classS4 class for tmod
tmod-dataDefault gene expression module data
tmodDecideTestsCount the Up- or Down-regulated genes per module
tmodImportMSigDBImport data from MSigDB
tmodLimmaDecideTestsUp- and down-regulated genes in modules based on limma object
tmodLimmaTestRun tmod enrichment tests directly on a limma object
tmodLimmaTopTabletmod's replacement for the limma topTable function
tmod-packageTranscriptional Module Analysis
tmodPalA selection of color palettes
tmodPanelPlotPlot a summary of multiple tmod analyses
tmodPCAPCA plot annotated with tmod
tmodSummaryCreate a summary of multiple tmod analyses
tmodTagcloudTag cloud based on tmod results
tmodUserGuideDisplay the tmod user guide
tmodUtestPerform a statistical test of module expression
tmod documentation built on May 2, 2019, 3 a.m.