Egambia                 Gene expression in TB patients and Healthy
                        controls
eigengene               Calculate the eigengene of a module from a data
                        set
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
length                  Shows the length of a tmod object
makeTmod                S4 class for tmod
makeTmodFromDataFrame   Convert a data frame to a tmod object
mbind                   Bind two or more transcriptional module sets
modCorPlot              Plot a correlation heatmap for modules
modGroups               Find group of modules
modOverlaps             Calculate overlaps of the modules
modcors                 Module correlation
modjaccard              Jaccard index for modules
modmetabo               Modules for metabolic profiling
mtx2mset                Convert between matrix representation of
                        modules and tmod objects
pcaplot                 Plot a PCA object returned by prcomp
pvalEffectPlot          Create an effect size / p-value plot
renameMods              Rename module IDs
show                    Shows the tmod object
showGene                A combined beeswarm / boxplot
showModule              Select genes belonging to a module from a data
                        frame
simplePie               Simple Pie Chart
tmod-data               Default gene expression module data
tmod-package            Transcriptional Module Analysis
tmod2DataFrame          Convert a tmod module set into a data frame
tmodAUC                 Calculate AUC
tmodDecideTests         Count the Up- or Down-regulated genes per
                        module
tmodImportMSigDB        Import data from MSigDB
tmodLEA                 Leading Edge Analysis
tmodLEASummary          Summary stats of a leading edge analysis
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
upset                   Upset plot
