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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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Version

Install

install.packages('tmod')

Monthly Downloads

239

Version

0.26

License

GPL (>= 2.0)

Maintainer

January Weiner

Last Published

May 17th, 2016

Functions in tmod (0.26)

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