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; Raymon Cao; Raymond Cheng; Matthew Satriano; Michael Considine; Gabriel Krigsfeld; Ruchira Ranaweera; Yong Tang; Sandra A. Jablonski; Genevieve Stein-O’Brien; Daria A. Gaykalova; Louis M. Weiner; Christine H. Chung; Elana J. Fertig

doi:10.1371/journal.pcbi.1006935

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, Raymon Cao, Raymond Cheng, Matthew Satriano, Michael Considine, Gabriel Krigsfeld, Ruchira Ranaweera, Yong Tang, Sandra A. Jablonski, Genevieve Stein-O’Brien, Daria A. Gaykalova, Louis M. Weiner, Christine H. Chung, Elana J. Fertig

School of Medicine

Research output: Contribution to journal › Article › peer-review

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)
Article number	e1006935
Journal	PLoS computational biology
Volume	15
Issue number	4
DOIs	https://doi.org/10.1371/journal.pcbi.1006935
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

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Sherman, T. D., Kagohara, L. T., Cao, R., Cheng, R., Satriano, M., Considine, M., Krigsfeld, G., Ranaweera, R., Tang, Y., Jablonski, S. A., Stein-O’Brien, G., Gaykalova, D. A., Weiner, L. M., Chung, C. H., & Fertig, E. J. (2019). Cancerinsilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS computational biology, 15(4), [e1006935]. https://doi.org/10.1371/journal.pcbi.1006935

Cancerinsilico : An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. / Sherman, Thomas D.; Kagohara, Luciane T.; Cao, Raymon; Cheng, Raymond; Satriano, Matthew; Considine, Michael; Krigsfeld, Gabriel; Ranaweera, Ruchira; Tang, Yong; Jablonski, Sandra A.; Stein-O’Brien, Genevieve; Gaykalova, Daria A.; Weiner, Louis M.; Chung, Christine H.; Fertig, Elana J.

In: PLoS computational biology, Vol. 15, No. 4, e1006935, 2019.

Research output: Contribution to journal › Article › peer-review

Sherman, TD, Kagohara, LT, Cao, R, Cheng, R, Satriano, M, Considine, M, Krigsfeld, G, Ranaweera, R, Tang, Y, Jablonski, SA, Stein-O’Brien, G, Gaykalova, DA, Weiner, LM, Chung, CH & Fertig, EJ 2019, 'Cancerinsilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer', PLoS computational biology, vol. 15, no. 4, e1006935. https://doi.org/10.1371/journal.pcbi.1006935

Sherman, Thomas D. ; Kagohara, Luciane T. ; Cao, Raymon ; Cheng, Raymond ; Satriano, Matthew ; Considine, Michael ; Krigsfeld, Gabriel ; Ranaweera, Ruchira ; Tang, Yong ; Jablonski, Sandra A. ; Stein-O’Brien, Genevieve ; Gaykalova, Daria A. ; Weiner, Louis M. ; Chung, Christine H. ; Fertig, Elana J. / Cancerinsilico : An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. In: PLoS computational biology. 2019 ; Vol. 15, No. 4.

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