Dataset Information

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

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.

SUBMITTER: McDonald TO

PROVIDER: S-EPMC5870718 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Publications

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

McDonald Thomas O TO Michor Franziska F

Bioinformatics (Oxford, England) 20170701 14

<h4>Summary</h4>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 ...[more]

PMID: 28334409

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Dataset Information

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

Summary

Availability and implementation

Supplementary information

Contact

Publications

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

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