# Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

## Documentation for package ‘tmod’ version 0.50.13

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

tmod-package | Transcriptional Module Analysis
as_tmodGS | S3 class for tmod gene set collections
cell_signatures | Cell type signatures
check_tmod_gs | Check an object of class tmodGS
Egambia | Gene expression in TB patients and Healthy controls
EgambiaResults | 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
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
length.tmodGS | S3 class for tmod gene set collections
makeTmod | S3 class for tmod gene set collections
makeTmodFromDataFrame | Convert a data frame to a tmod object
makeTmodGS | S3 class for tmod gene set collections
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
pcaplot | Plot a PCA object returned by prcomp
print.tmodGS | S3 class for tmod gene set collections
pvalEffectPlot | Create an effect size / p-value plot
showGene | A combined beeswarm / boxplot
showModule | Filter by genes belonging to a gene set 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-data | Default gene expression module data
tmod2DataFrame | Convert a tmod module set into a data frame
tmod2tmodGS | Convert the old tmod objects to the tmodGS objects
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
tmodZtest | Perform a statistical test of module expression
tmod_ids | Query and set IDs of gene sets in a tmodGS object
tmod_ids<- | Query and set IDs of gene sets in a tmodGS object
tmod_titles | Query and set IDs of gene sets in a tmodGS object
tmod_titles<- | Query and set IDs of gene sets in a tmodGS object
upset | Upset plot
vaccination | Transcriptomic responses to vaccination
[.tmod | S3 class for tmod gene set collections
[.tmodGS | S3 class for tmod gene set collections