Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <doi:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <doi:10.1093/molbev/msaa053>.
| Version: | 4.4.0 |
| Imports: | bigutilsr (≥ 0.3), data.table, ggplot2, magrittr, mmapcharr (≥ 0.3), Rcpp (≥ 0.12.8), RSpectra |
| LinkingTo: | mmapcharr, Rcpp, rmio |
| Suggests: | plotly, shiny, spelling, testthat, vcfR |
| Published: | 2024-09-24 |
| DOI: | 10.32614/CRAN.package.pcadapt |
| Author: | Keurcien Luu [aut], Michael Blum [aut], Florian Privé [aut, cre], Eric Bazin [ctb], Nicolas Duforet-Frebourg [ctb] |
| Maintainer: | Florian Privé <florian.prive.21 at gmail.com> |
| BugReports: | https://github.com/bcm-uga/pcadapt/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/bcm-uga/pcadapt |
| NeedsCompilation: | yes |
| Language: | en-US |
| Citation: | pcadapt citation info |
| Materials: | README NEWS |
| CRAN checks: | pcadapt results |
| Reference manual: | pcadapt.pdf |
| Package source: | pcadapt_4.4.0.tar.gz |
| Windows binaries: | r-devel: pcadapt_4.4.0.zip, r-release: pcadapt_4.4.0.zip, r-oldrel: pcadapt_4.4.0.zip |
| macOS binaries: | r-devel (arm64): pcadapt_4.4.0.tgz, r-release (arm64): pcadapt_4.4.0.tgz, r-oldrel (arm64): pcadapt_4.4.0.tgz, r-devel (x86_64): pcadapt_4.4.0.tgz, r-release (x86_64): pcadapt_4.4.0.tgz, r-oldrel (x86_64): pcadapt_4.4.0.tgz |
| Old sources: | pcadapt archive |
| Reverse suggests: | bigsnpr |
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