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tmod (version 0.19)
Transcriptional Module Analysis
Description
The tmod package contains definitions of human blood transcriptional modules and tools to analyse them.
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0.50.13
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0.19
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Install
install.packages('tmod')
Monthly Downloads
370
Version
0.19
License
GPL (>= 2.0)
Maintainer
January Weiner
Last Published
June 19th, 2015
Functions in tmod (0.19)
Search functions
show
Shows the tmod object
tmod-class
An S4 class that stores modules.
tmodDecideTests
Count the Up- or Down-regulated genes per module
Egambia
Gene expression in TB patients and Healthy controls
tmodTagcloud
Tag cloud based on tmod results
simplePie
Simple Pie Chart
showModule
Select genes belonging to a module from a data frame
pvalEffectPlot
Create an effect size / p-value plot
tmodLimmaDecideTests
Up- and down-regulated genes in modules based on limma object
tmodLimmaTopTable
tmod's replacement for the limma topTable function
tmodImportMSigDB
Import data from MSigDB
tmodPanelPlot
Plot a summary of multiple tmod analyses
tmodPCA
PCA plot annotated with tmod
hgEnrichmentPlot
Create a visualisation of enrichment
tmodAUC
Calculate AUC
tmodSummary
Create a summary of multiple tmod analyses
getGenes
Get genes belonging to a module
tmodUtest
Perform a statistical test of module expression
evidencePlot
Create an evidence plot for a module
tmod-package
Transcriptional Module Analysis
showGene
A combined beeswarm / boxplot
tmodLimmaTest
Run tmod enrichment tests directly on a limma object