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tmod (version 0.26)
Transcriptional Module Analysis
Description
Gene set enrichment analysis tools and definitions of human blood transcriptional modules.
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0.50.13
0.50.11
0.46.2
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0.36
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0.30
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0.26
0.24
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Install
install.packages('tmod')
Monthly Downloads
433
Version
0.26
License
GPL (>= 2.0)
Maintainer
January Weiner
Last Published
May 17th, 2016
Functions in tmod (0.26)
Search functions
showModule
Select genes belonging to a module from a data frame
getModuleMembers
Return the contents of a module
showGene
A combined beeswarm / boxplot
tmodAUC
Calculate AUC
makeTmod
S4 class for tmod
Egambia
Gene expression in TB patients and Healthy controls
show
Shows the tmod object
hgEnrichmentPlot
Create a visualisation of enrichment
getGenes
Get genes belonging to a module
evidencePlot
Create an evidence plot for a module
tmodLimmaTopTable
tmod's replacement for the limma topTable function
tmodPanelPlot
Plot a summary of multiple tmod analyses
tmod-package
Transcriptional Module Analysis
tmodDecideTests
Count the Up- or Down-regulated genes per module
tmodUtest
Perform a statistical test of module expression
tmodPCA
PCA plot annotated with tmod
simplePie
Simple Pie Chart
tmodSummary
Create a summary of multiple tmod analyses
pvalEffectPlot
Create an effect size / p-value plot
tmodLimmaTest
Run tmod enrichment tests directly on a limma object
tmodTagcloud
Tag cloud based on tmod results
tmodImportMSigDB
Import data from MSigDB
tmod-data
Default gene expression module data
tmodLimmaDecideTests
Up- and down-regulated genes in modules based on limma object