NetworkDataCompanion

This package is part of the Reproducible processing of TCGA regulatory networks paper available on BioRxiv

• NetworkDataCompanion is an R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo
• NetworkDataCompanion is also the engine behind the tcga-data-nf workflow
• The code for tcga-data-nf is available in the QuackenbushLab GitHub: https://github.com/QuackenbushLab/tcga-data-nf

Installing

You can install this package with devtools using the following code:

library(devtools)
devtools::install_github("QuackenbushLab/NetworkDataCompanion")
library(NetworkDataCompanion)

If you want to work with the source, you can also clone the repository and install it from the root directory locally once you have done so.

library(devtools)
devtools::install()  # provided you are in the project folder
library(NetworkDataCompanion) 

We have noticed that sometimes the following packages may require separate installation: "GenomicDataCommons", "edgeR", "recount", "recount3". If you have problems with these, please raise an issue here: https://github.com/QuackenbushLab/NetworkDataCompanion/issues or directly and/contact the maintainer (Kate Shutta, kshutta at hsph.harvard.edu).

Usage

• A quickstart guide is located in the base directory (quickstart.Rmd and quickstart.html).
• You can view the rendered html of the quickstart here: NetworkDataCompanion Quickstart
• Example usage of all functions is also available in the unit tests: https://github.com/QuackenbushLab/NetworkDataCompanion/tree/main/tests/testthat

Structure of the repo

• R contains the source code of our functions.
• tests contains extensive tests of the implemented functions.
• inst contains external data needed to run the analyses on TCGA and GTEx (e.g., gene mapping files)
• man is used to generate documentation.

Citation

@article{fanfani2024reproducible,
  title={Reproducible processing of TCGA regulatory networks},
  author={Fanfani, Viola and Shutta, Katherine H and Mandros, Panagiotis and Fischer, Jonas and Saha, Enakshi and Micheletti, Soel and Chen, Chen and Ben Guebila, Marouen and Lopes-Ramos, Camila Miranda and Quackenbush, John},
  journal={bioRxiv},
  pages={2024--11},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

If you find this package useful, feel free to star this repository!