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

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

gene regulatory networks, co-expression methods, differential network analysis,
Gaussian graphical model

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
from the Comprehensive R Archive Network at https://CRAN.R-project.org/package=
SeqNet and on GitHub at https://github.com/tgrimes/SeqNet.

Tyler Grimes

https://www.jstatsoft.org/article/view/v098i12

University of North Florida

May 2021

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