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PeerJ. 2019 May 23;7:e6985. doi: 10.7717/peerj.6985. eCollection 2019.

Simphony: simulating large-scale, rhythmic data.

Author information

1
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States of America.
2
Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America.

Abstract

Simulated data are invaluable for assessing a computational method's ability to distinguish signal from noise. Although many biological systems show rhythmicity, there is no general-purpose tool to simulate large-scale, rhythmic data. Here we present Simphony, an R package for simulating data from experiments in which the abundances of rhythmic and non-rhythmic features (e.g., genes) are measured at multiple time points in multiple conditions. Simphony has parameters for specifying experimental design and each feature's rhythmic properties (e.g., amplitude and phase). In addition, Simphony can sample measurements from Gaussian and negative binomial distributions, the latter of which approximates read counts from RNA-seq data. We show an example of using Simphony to evaluate the accuracy of rhythm detection. Our results suggest that Simphony will aid experimental design and computational method development. Simphony is thoroughly documented and freely available at https://github.com/hugheylab/simphony.

KEYWORDS:

Circadian; Gene expression; Rhythms; Simulation; Transcriptome

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