retroData: companion data package for the article "The effect of statistical normalization on network propagation scores", https://doi.org/10.1093/bioinformatics/btaa896

Install

For the development version, change directory to the retroData path and execute

devtools::install()

You can also install the package through the built zip file

R CMD INSTALL retroData_0.2.0.tar.gz

or through its GitHub repository.

Getting started

Have a glance at the package help

?retroData

List of data objects from the three main sections in the article:

1. Yeast analysis:

• yeast: network

2. Simulated gene expression analysis:

• interactome: network
• ALL: gene background
• dataLym: gene background
• keggdlbcl: KEGG gene sets from 2017

3. Prospective pathway prediction:

• biogrid2011 PPI network from before 2011
• kegg2011: KEGG pathways from 2011
• kegg2018: KEGG pathways from 2018

The code to perform the analysis can be found in our diffuBench repository.

Please note that the data come from various sources and are provided for reproducibility of the original manuscript. Only the necessary files are provided, and any further use of the data should adhere to the licensing terms of its source.