slendr (Q71149): Difference between revisions
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Removed claim: imports (P585): ggplot2 (Q57344) |
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Property / last update: 9 March 2023 / rank | |||||||||||||||
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Property / cites work: SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model / rank | |||||||||||||||
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Property / cites work: Efficient ancestry and mutation simulation with msprime 1.0 / rank | |||||||||||||||
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Property / cites work: Inferring whole-genome histories in large population datasets / rank | |||||||||||||||
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publication date: 9 August 2022
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publication date: 19 August 2022
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publication date: 30 September 2022
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publication date: 3 February 2023
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publication date: 7 June 2023
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publication date: 26 June 2023
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publication date: 14 July 2023
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publication date: 8 August 2023
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publication date: 7 December 2023
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publication date: 15 January 2024
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publication date: 8 February 2024
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publication date: 21 February 2024
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21 February 2024
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A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis. | |||||||||||||||
Property / description: A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis. / rank | |||||||||||||||
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Property / author: Martin Petr / rank | |||||||||||||||
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Property / cites work: SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model / rank | |||||||||||||||
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Property / cites work: Efficient ancestry and mutation simulation with msprime 1.0 / rank | |||||||||||||||
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Property / cites work: Inferring whole-genome histories in large population datasets / rank | |||||||||||||||
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software version identifier: ≥ 3.6.0 | |||||||||||||||
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Latest revision as of 19:56, 12 March 2024
A Simulation Framework for Spatiotemporal Population Genetics
Language | Label | Description | Also known as |
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English | slendr |
A Simulation Framework for Spatiotemporal Population Genetics |
Statements
21 February 2024
0 references
A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.
0 references