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 |
makeTmodFromDataFrame | Convert a data frame to a tmod object |
mbind | Bind two or more transcriptional module sets |
modCorPlot | Plot a correlation heatmap for modules |
modcors | Module correlation |
modGroups | Find group of modules |
modjaccard | Jaccard index for modules |
modmetabo | Modules for metabolic profiling |
modOverlaps | Calculate overlaps of the modules |
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 |
tmod2DataFrame | Convert a tmod module set into a data frame |
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 |
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 |
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 |
tmodUtest | Perform a statistical test of module expression |
tmodWZtest | Perform a statistical test of module expression |
tmodZtest | Perform a statistical test of module expression |
upset | Upset plot |
vaccination | Transcriptomic responses to vaccination |
[-method | Shows the tmod object |