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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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Version

Install

install.packages('tmod')

Monthly Downloads

286

Version

0.19

License

GPL (>= 2.0)

Maintainer

January Weiner

Last Published

June 19th, 2015

Functions in tmod (0.19)

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