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Bioinformatics. 2017 Jul 15;33(14):2221-2223. doi: 10.1093/bioinformatics/btx146.

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

Author information

1
Department of Biostatistics and Computational Biology, Center for Cancer Evolution, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

Abstract

Summary:

SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own.

Availability and Implementation:

SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ).

Supplementary information:

Supplementary data are available at Bioinformatics online.

Contact:

michor@jimmy.harvard.edu.

PMID:
28334409
PMCID:
PMC5870718
DOI:
10.1093/bioinformatics/btx146
[Indexed for MEDLINE]
Free PMC Article

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