Abstract
Bioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The absence of a known ground truth of the dynamics of molecular changes challenges benchmarking their performance on real data. Realistic simulated time-course datasets are essential to assess the performance of time course bioinformatics algorithms. We develop an R/Bioconductor package, CancerInSilico, to simulate bulk and single cell transcriptional data from a known ground truth obtained from mathematical models of cellular systems. This package contains a general R infrastructure for running cell-based models and simulating gene expression data based on the model states. We show how to use this package to simulate a gene expression data set and consequently benchmark analysis methods on this data set with a known ground truth. The package is freely available via Bioconductor: http://bioconductor.org/packages/CancerInSilico/.
Original language | English (US) |
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Article number | e1006935 |
Journal | PLoS computational biology |
Volume | 15 |
Issue number | 4 |
DOIs | |
State | Published - 2019 |
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Modeling and Simulation
- Ecology
- Molecular Biology
- Genetics
- Cellular and Molecular Neuroscience
- Computational Theory and Mathematics