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tmod

tmod – Gene set enrichments

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Version

Install

install.packages('tmod')

Monthly Downloads

286

Version

0.44

License

GPL (>= 2.0)

Maintainer

January Weiner

Last Published

June 18th, 2020

Functions in tmod (0.44)

Create an effect size / p-value plot

Find group of modules

Plot a correlation heatmap for modules

Rename module IDs

Modules for metabolic profiling

Jaccard index for modules

A combined beeswarm / boxplot

Select genes belonging to a module from a data frame

S4 class for tmod

Simple Pie Chart

Convert between matrix representation of modules and tmod objects

Plot a PCA object returned by prcomp

Calculate the eigengene of a module from a data set

A selection of color palettes

tmodLimmaTopTable

tmod's replacement for the limma topTable function

Convert a tmod module set into a data frame

Plot a summary of multiple tmod analyses

Create a summary of multiple tmod analyses

Calculate overlaps of the modules

Tag cloud based on tmod results

tmodLimmaDecideTests

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

Run tmod enrichment tests directly on a limma object

Module correlation

Transcriptional Module Analysis

Default gene expression module data

Perform a statistical test of module expression

tmodDecideTests

Count the Up- or Down-regulated genes per module

PCA plot annotated with tmod

tmodImportMSigDB

Import data from MSigDB

Summary stats of a leading edge analysis

Leading Edge Analysis

hgEnrichmentPlot

Create a visualisation of enrichment

Get genes belonging to a module

makeTmodFromDataFrame

Convert a data frame to a tmod object

Gene expression in TB patients and Healthy controls

Create an evidence plot for a module

Bind two or more transcriptional module sets

Shows the length of a tmod object

getModuleMembers

Return the contents of a module

Shows the tmod object