CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
Thomas D Sherman,
Luciane T Kagohara,
Sandra A Jablonski,
Daria A Gaykalova,
Louis M Weiner,
Christine H Chung,
Elana J. Fertig
Posted 23 May 2018
bioRxiv DOI: 10.1101/328807 (published DOI: 10.1371/journal.pcbi.1006935)
Posted 23 May 2018
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/
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