Man pages for tmod
Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
| cell_signatures | Cell type signatures |
| check_tmod_gs | Check an object of class tmodGS |
| 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 |
| 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 |
| 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 |
| pvalEffectPlot | Create an effect size / p-value plot |
| showGene | A combined beeswarm / boxplot |
| simplePie | Simple Pie Chart |
| tmod2DataFrame | Convert a tmod module set into a data frame |
| tmod2tmodGS | Convert the old tmod objects to the tmodGS objects |
| tmodAUC | Calculate AUC |
| tmod-data | Default gene expression module data |
| tmodDecideTests | Count the Up- or Down-regulated genes per module |
| tmodGS-class | S3 class for tmod gene set collections |
| tmod_ids | Query and set IDs of gene sets in a tmodGS object |
| 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 |
| tmod-package | Transcriptional Module Analysis |
| 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 |
| upset | Upset plot |
| vaccination | Transcriptomic responses to vaccination |
