tmod0.50.13 package

Check an object of class tmodGS

Calculate the eigengene of a module from a data set

Create an evidence plot for a module

Filter by genes belonging to a gene set from a data frame

Get genes belonging to a gene set

Return the contents of a gene set

Create an evidence plot for a module (ggplot2 version)

Create a tmod panel plot using ggplot

Create a visualisation of enrichment

Convert a data frame to a tmod object

Plot a correlation heatmap for modules

Module correlation

Find group of modules

Jaccard index for modules

Calculate overlaps of the modules

Plot a PCA object returned by prcomp

Create an effect size / p-value plot

A combined beeswarm / boxplot

Simple Pie Chart

Default gene expression module data

Transcriptional Module Analysis

Query and set IDs of gene sets in a tmodGS object

Convert a tmod module set into a data frame

Convert the old tmod objects to the tmodGS objects

Calculate AUC

Count the Up- or Down-regulated genes per module

S3 class for tmod gene set collections

Import data from MSigDB

Leading Edge Analysis

Summary stats of a leading edge analysis

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

Run tmod enrichment tests directly on a limma object

tmod's replacement for the limma topTable function

A selection of color palettes

Plot a summary of multiple tmod analyses

PCA plot annotated with tmod

Create a summary of multiple tmod analyses

Tag cloud based on tmod results

Perform a statistical test of module expression

Upset plot