tmod-package | Transcriptional Module Analysis |
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 |
show-method | Shows the tmod object |
showGene | A combined beeswarm / boxplot |
showModule | Select genes belonging to a module from a data frame |
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 |
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 |
tmodSummary | Create a summary of multiple tmod analyses |
tmodTagcloud | Tag cloud based on tmod results |
tmodUtest | Perform a statistical test of module expression |
[ | Shows the tmod object |
[-method | Shows the tmod object |