ViDGER

Overview

ViDGER (Visualization of Differential Gene Expression using R), is an R package that can rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Installation

The stable version of this package is available on Bioconductor . You can install it by:

if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("vidger")

If you want the latest version, install it directly from this GitHub repo:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("btmonier/vidger", ref = "devel")

Functions

The stable release of vidger has 9 visualization functions:

vsScatterPlot()
vsScatterMatrix()
vsBoxplot()
vsDEGMatrix()
vsVolcano()
vsVolcanoMatrix()
vsMAPlot()
vsMAMatrix()
vsFourWay()

Loading test data

To simulate the usage of the three aformentioned tools, "toy" data sets have been implemented in this package. Each of these data sets represents their respective R class:

df.cuff A cuffdiff output file.
df.deseq A DESeq2 object class.
df.edger An edgeR object class.

To load these data sets, use the following command:

data("<object-type>")

...where "<object-type>" is one of the previously mentioned data sets.

Getting help

For additional information on these functions, please see the given documentation in the vidger package by adding the ? help operator before any of the given functions in this package or by using the help() function.

For a more in-depth analysis, consider reading the vignette provided with this package:

vignette("vidger")

Last updated: 2019-01-18