pcadapt
R package {pcadapt} has been developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA).
A tutorial for {pcadapt} is available on pcadapt's website.
News: A new paper is finally out describing version 4 of pcadapt (which has been available for quite some time now). Please cite the new paper.
Installation
# From CRAN
install.packages("pcadapt")
# From GitHub
remotes::install_github("bcm-uga/pcadapt")References
Privé, F., Luu, K., Vilhjálmsson, B. J., & Blum, M. G.B. (2020). Performing highly efficient genome scans for local adaptation with R package pcadapt version 4. Molecular Biology and Evolution.
Luu, K., Bazin, E., & Blum, M. G.B. (2017). pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources, 17(1), 67-77.
Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E., & Blum, M. G.B. (2015). Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular biology and evolution, 33(4), 1082-1093.