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

cell_signaturesCell type signatures
check_tmod_gsCheck an object of class tmodGS
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
filterGSFilter by genes belonging to a gene set from a data frame
getGenesGet genes belonging to a gene set
getModuleMembersReturn the contents of a gene set
ggEvidencePlotCreate an evidence plot for a module (ggplot2 version)
ggPanelplotCreate a tmod panel plot using ggplot
hgEnrichmentPlotCreate a visualisation of enrichment
makeTmodFromDataFrameConvert a data frame to a tmod object
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
pcaplotPlot a PCA object returned by prcomp
pvalEffectPlotCreate an effect size / p-value plot
showGeneA combined beeswarm / boxplot
simplePieSimple Pie Chart
tmod2DataFrameConvert a tmod module set into a data frame
tmod2tmodGSConvert the old tmod objects to the tmodGS objects
tmodAUCCalculate AUC
tmod-dataDefault gene expression module data
tmodDecideTestsCount the Up- or Down-regulated genes per module
tmodGS-classS3 class for tmod gene set collections
tmod_idsQuery and set IDs of gene sets in a tmodGS object
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 March 31, 2023, 9 p.m.