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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: | 4.3.5 |
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: | 2023-08-29 |
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_4.3.5.tar.gz |
Windows binaries: | r-devel: pcadapt_4.3.5.zip, r-release: pcadapt_4.3.5.zip, r-oldrel: pcadapt_4.3.5.zip |
macOS binaries: | r-release (arm64): pcadapt_4.3.5.tgz, r-oldrel (arm64): pcadapt_4.3.5.tgz, r-release (x86_64): pcadapt_4.3.5.tgz, r-oldrel (x86_64): pcadapt_4.3.5.tgz |
Old sources: | pcadapt archive |
Reverse suggests: | bigsnpr |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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