EgambiaResults          Gene expression in TB patients and Healthy
                        controls
cell_signatures         Cell type signatures
check_tmod_gs           Check an object of class tmodGS
eigengene               Calculate the eigengene of a module from a data
                        set
evidencePlot            Create an evidence plot for a module
filterGS                Filter by genes belonging to a gene set from a
                        data frame
getGenes                Get genes belonging to a gene set
getModuleMembers        Return the contents of a gene set
ggEvidencePlot          Create an evidence plot for a module (ggplot2
                        version)
ggPanelplot             Create a tmod panel plot using ggplot
hgEnrichmentPlot        Create a visualisation of enrichment
makeTmodFromDataFrame   Convert a data frame to a tmod object
makeTmodGS              S3 class for tmod gene set collections
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
pcaplot                 Plot a PCA object returned by prcomp
pvalEffectPlot          Create an effect size / p-value plot
showGene                A combined beeswarm / boxplot
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
tmod2tmodGS             Convert the old tmod objects to the tmodGS
                        objects
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
tmod_ids                Query and set IDs of gene sets in a tmodGS
                        object
upset                   Upset plot
vaccination             Transcriptomic responses to vaccination
