| tmod-package | Transcriptional Module Analysis |
| 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 |
| length-method | Shows the length of a tmod object |
| makeTmod | S4 class for tmod |
| mbind | Bind two or more transcriptional module sets |
| modcors | Module correlation |
| modjaccard | Jaccard index for modules |
| modmetabo | Modules for metabolic profiling |
| mset2mtx | Convert between matrix representation of modules and tmod objects |
| 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 |
| show-method | Shows the tmod object |
| showGene | A combined beeswarm / boxplot |
| showModule | Select genes belonging to a module from a data frame |
| simpleBoxpie | Simple Pie Chart |
| simplePie | Simple Pie Chart |
| simpleRug | Simple Pie Chart |
| tbmprof | Modules for metabolic profiling |
| tmod | Default gene expression module data |
| tmod-class | S4 class for tmod |
| tmod-data | Default gene expression module data |
| tmodAUC | Calculate AUC |
| tmodCERNOtest | Perform a statistical test of module expression |
| tmodDecideTests | Count the Up- or Down-regulated genes per module |
| tmodGeneSetTest | Perform a statistical test of module expression |
| tmodHGtest | Perform a statistical test of module expression |
| 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 |
| tmodPal | A selection of color palettes |
| tmodPanelPlot | Plot a summary of multiple tmod analyses |
| tmodPCA | PCA plot annotated with tmod |
| tmodPLAGEtest | Perform a statistical test of module expression |
| tmodSummary | Create a summary of multiple tmod analyses |
| tmodTagcloud | Tag cloud based on tmod results |
| tmodUserGuide | Display the tmod user guide |
| tmodUtest | Perform a statistical test of module expression |
| tmodWZtest | Perform a statistical test of module expression |
| tmodZtest | Perform a statistical test of module expression |
| [-method | Shows the tmod object |