Egambia                 Gene expression in TB patients and Healthy
                        controls
evidencePlot            Create an evidence plot for a module
getGenes                Get genes belonging to a module
getModuleMembers        Return the contents of a module
hgEnrichmentPlot        Create a visualisation of enrichment
makeTmod                S4 class for tmod
modmetabo               Modules for metabolic profiling
pvalEffectPlot          Create an effect size / p-value plot
show                    Shows the tmod object
showGene                A combined beeswarm / boxplot
showModule              Select genes belonging to a module from a data
                        frame
tmod-data               Default gene expression module data
tmod-package            Transcriptional Module Analysis
tmodAUC                 Calculate AUC
tmodDecideTests         Count the Up- or Down-regulated genes per
                        module
tmodImportMSigDB        Import data from MSigDB
tmodLimmaDecideTests    Up- and down-regulated genes in modules based
                        on limma object
tmodLimmaTest           Run tmod enrichment tests directly on a limma
                        object
tmodLimmaTopTable       tmod's replacement for the limma topTable
                        function
tmodPCA                 PCA plot annotated with tmod
tmodPal                 A selection of color palettes
tmodPanelPlot           Plot a summary of multiple tmod analyses
tmodSummary             Create a summary of multiple tmod analyses
tmodTagcloud            Tag cloud based on tmod results
tmodUtest               Perform a statistical test of module expression
