sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

BMC Bioinformatics

Jason Lloyd-Price¹  Matthias Dehmer²  Olli Yli-Harja³  Andre Ribeiro⁴  Frank Emmert-Streib⁵  Shailesh Tripathi⁵ 

[1] Department of Biostatistics, Harvard T.H. Chan School of Public Health;Institute for Theoretical Informatics, Mathematics and Operations Research, Department of Computer Science, Universität der Bundeswehr München;Institute of Biosciences and Medical Technology;Laboratory of Biosystem Dynamics, Department of Signal Processing;Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology;

关键词: Gene expression data;    Gene network;    Simulation;   

DOI  :  10.1186/s12859-017-1731-8

来源: DOAJ

【 摘 要 】

Abstract Background sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles. Results The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. Conclusions sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X.

【 授权许可】

Unknown