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tmod (version 0.24)
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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Install
install.packages('tmod')
Monthly Downloads
370
Version
0.24
License
GPL (>= 2.0)
Maintainer
January Weiner
Last Published
February 26th, 2016
Functions in tmod (0.24)
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getGenes
Get genes belonging to a module
evidencePlot
Create an evidence plot for a module
tmodAUC
Calculate AUC
pvalEffectPlot
Create an effect size / p-value plot
show
Shows the tmod object
tmodPCA
PCA plot annotated with tmod
tmodLimmaTopTable
tmod's replacement for the limma topTable function
Egambia
Gene expression in TB patients and Healthy controls
makeTmod
S4 class for tmod
tmod-package
Transcriptional Module Analysis
tmodLimmaTest
Run tmod enrichment tests directly on a limma object
simplePie
Simple Pie Chart
hgEnrichmentPlot
Create a visualisation of enrichment
tmodDecideTests
Count the Up- or Down-regulated genes per module
tmodSummary
Create a summary of multiple tmod analyses
tmod-data
Default gene expression module data
tmodImportMSigDB
Import data from MSigDB
tmodUtest
Perform a statistical test of module expression
tmodPanelPlot
Plot a summary of multiple tmod analyses
tmodLimmaDecideTests
Up- and down-regulated genes in modules based on limma object
showGene
A combined beeswarm / boxplot
tmodTagcloud
Tag cloud based on tmod results
getModuleMembers
Return the contents of a module
showModule
Select genes belonging to a module from a data frame