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
makeTmodFromDataFrameConvert a data frame to a tmod object
mbindBind two or more transcriptional module sets
modCorPlotPlot a correlation heatmap for modules
modcorsModule correlation
modGroupsFind group of modules
modjaccardJaccard index for modules
modmetaboModules for metabolic profiling
modOverlapsCalculate overlaps of the modules
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
tmod2DataFrameConvert a tmod module set into a data frame
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
tmodLEALeading Edge Analysis
tmodLEASummarySummary stats of a leading edge analysis
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
tmodUtestPerform a statistical test of module expression
upsetUpset plot
vaccinationTranscriptomic responses to vaccination
tmod documentation built on Oct. 23, 2020, 6:12 p.m.