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

Tyler Grimes, Somnath Datta

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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 SeqNet and on GitHub at

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