Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Tyler Grimes, Somnath Datta
Title: SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data
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 from the Comprehensive R Archive Network at https://CRAN.R-project.org/package= SeqNet and on GitHub at https://github.com/tgrimes/SeqNet.

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Paper: SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data     Download PDF (Downloads: 89)
Supplements:
SeqNet_1.1.3.tar.gz: R source package Download (Downloads: 2; 4MB)
v98i12-replication.zip: Replication materials Download (Downloads: 3; 91MB)

DOI: 10.18637/jss.v098.i12

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.