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 |