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tmod (version 0.30)

Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Description

Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis.

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Version

Install

install.packages('tmod')

Monthly Downloads

231

Version

0.30

License

GPL (>= 2.0)

Maintainer

January Weiner

Last Published

August 5th, 2016

Functions in tmod (0.30)

modmetabo

Modules for metabolic profiling
getGenes

Get genes belonging to a module
showModule

Select genes belonging to a module from a data frame
Egambia

Gene expression in TB patients and Healthy controls
hgEnrichmentPlot

Create a visualisation of enrichment
pvalEffectPlot

Create an effect size / p-value plot
showGene

A combined beeswarm / boxplot
evidencePlot

Create an evidence plot for a module
show

Shows the tmod object
getModuleMembers

Return the contents of a module
simplePie

Simple Pie Chart
tmodLimmaTest

Run tmod enrichment tests directly on a limma object
tmodLimmaTopTable

tmod's replacement for the limma topTable function
tmod-package

Transcriptional Module Analysis
tmodAUC

Calculate AUC
tmod-data

Default gene expression module data
tmodDecideTests

Count the Up- or Down-regulated genes per module
tmodLimmaDecideTests

Up- and down-regulated genes in modules based on limma object
makeTmod

S4 class for tmod
tmodImportMSigDB

Import data from MSigDB
tmodPal

A selection of color palettes
tmodPanelPlot

Plot a summary of multiple tmod analyses
tmodPCA

PCA plot annotated with tmod
tmodUtest

Perform a statistical test of module expression
tmodSummary

Create a summary of multiple tmod analyses
tmodTagcloud

Tag cloud based on tmod results