SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data – Tyler Grimes

Authors

Tyler Grimes

Somnath Datta

Published

July 10, 2021

In Journal of Statistical Software

Abstract

Gene expression data provide an abundant resource for inferring connections in gene regulatory networks. While methodologies developed for this task have shown success, a challenge remains in comparing the performance among methods. Gold-standard datasets are scarce and limited in use. And while tools for simulating expression data are available, they are not designed to resemble the data obtained from RNA-seq experiments. SeqNet is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods. The package is available on CRAN and on GitHub at https://github.com/tgrimes/SeqNet.

Summary

SeqNet is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods.

doi: 10.18637/jss.v098.i12

SeqNet R package available on CRAN

---
title: "SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data"
date: 2021-07-10
draft: false
authors: ["Tyler Grimes", "Somnath Datta"]
tags: ["Simulation", "RNA-seq", "Graphical models"]
image: "featured.png"
---

In [*Journal of Statistical Software*](https://www.jstatsoft.org/article/view/v098i12)

![](featured.png)

## Abstract

Gene expression data provide an abundant resource for inferring connections in gene regulatory networks. While methodologies developed for this task have shown success, a challenge remains in comparing the performance among methods. Gold-standard datasets are scarce and limited in use. And while tools for simulating expression data are available, they are not designed to resemble the data obtained from RNA-seq experiments. SeqNet is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods. The package is available on CRAN and on GitHub at https://github.com/tgrimes/SeqNet.

## Summary

`SeqNet` is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods.

doi: [10.18637/jss.v098.i12](10.18637/jss.v098.i12)

`SeqNet` R package [available on CRAN](https://cran.r-project.org/web/packages/SeqNet/index.html)