Package: pcadapt 4.4.0

Florian Privé

pcadapt: Fast Principal Component Analysis for Outlier Detection

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>.

Authors:Keurcien Luu [aut], Michael Blum [aut], Florian Privé [aut, cre], Eric Bazin [ctb], Nicolas Duforet-Frebourg [ctb]

pcadapt_4.4.0.tar.gz
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pcadapt.pdf |pcadapt.html
pcadapt/json (API)
NEWS

# Install 'pcadapt' in R:
install.packages('pcadapt', repos = c('https://bcm-uga.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bcm-uga/pcadapt/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

7.76 score 39 stars 293 scripts 1.1k downloads 64 mentions 14 exports 50 dependencies

Last updated 2 months agofrom:792610704b. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64OKNov 02 2024
R-4.5-linux-x86_64OKNov 02 2024
R-4.4-win-x86_64OKNov 02 2024
R-4.4-mac-x86_64OKNov 02 2024
R-4.4-mac-aarch64OKNov 02 2024
R-4.3-win-x86_64OKNov 02 2024
R-4.3-mac-x86_64OKNov 02 2024
R-4.3-mac-aarch64OKNov 02 2024

Exports:bed2matrixget.pcget.pop.namesget.score.colorhist_plotmanhattan_plotpcadaptqq_plotread.pcadaptrun.pcadaptscore_plotscree_plotvcf2pcadaptwriteBed

Dependencies:BHbigassertrbigparallelrbigutilsrbitclicodetoolscolorspacedata.tableDEoptimRdoParallelfansifarverffflockforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmmapcharrmunsellnabornlmeparallellypillarpkgconfigR6RColorBrewerRcppRcppEigenRhpcBLASctlrlangrmiorobustbaseRSpectrascalestibbleutf8vctrsviridisLitewithr