rBAPS

R implementation of the compiled Matlab BAPS software for Bayesian Analysis of Population Structure.

Installation

rBAPS is currently under development and a stable version is yet to be released. You can install the development version by issuing the command below on an interactive R session.

remotes::install_github("ocbe-uio/rBAPS", "dev")

Contributing

rBAPS is Open Software licenced under the GPL-3, so all contributions are welcome. You can find a list of todos and pitfalls on the TODO.md file.

References

How to cite this project

After installing the package, issue citation("rBAPS") in R. You will get a pure text and a BibTeX entry of rBAPS. Alternatively, you can use the CITATION.cff file, which conforms to the (Citation File Format)[https://citation-file-format.github.io/] standard.

Scientific papers

These are some of the scientific publications that served as base for the creation of rBAPS:

Corander, J. and Marttinen, P. (2006), Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology, 15: 2833-2843. doi:10.1111/j.1365-294X.2006.02994.x
Corander, J., Sirén, J., & Arjas, E. (2008). Bayesian spatial modeling of genetic population structure. Computational Statistics, 23(1), 111-129. doi:10.1007/s00180-007-0072-x
Corander, J., Marttinen, P., Sirén, J. et al. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9, 539 (2008) doi:10.1186/1471-2105-9-539
Tonkin-Hill G, Lees JA, Bentley SD et al. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS [version 1; peer review: 2 approved]. Wellcome Open Res 2018, 3:93 (https://doi.org/10.12688/wellcomeopenres.14694.1)

Software

Below we list some of the software directly related to rBAPS:

2.4 KiB Raw Blame History