No packages match

slendr - A Simulation Framework for Spatiotemporal Population Genetics

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.

Last updated

popgenpopulation-geneticssimulationsspatial-statistics

9.52 score 63 stars 144 scripts 266 downloads

admixr - An Interface for the Software Package 'ADMIXTOOLS'

An interface for various command-line tools provided by the software suite 'ADMIXTOOLS' (<https://github.com/DReichLab/AdmixTools>). Wrapper functions completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line in the background, and extract statistics of interest from plain-text files which they produce. This allows users to avoid dealing with low-level technical details of shell scripting (which is requried by traditional 'ADMIXTOOLS' workflows) and focus on their research problem at hand instead. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.

Last updated

bioinformaticspopgenpopulation-genetics

7.49 score 37 stars 84 scripts 376 downloads