adegenet

a R package for the multivariate analysis of genetic markers

in R package

Adegenet was created by Thibaut Jombart and has been on CRAN since April, 2007. I was involved in the migration to version 2.0 in the summer of 2015, which included consolitading S4 methods and including the strata() methods.

I have been maintaining the package by fixing bugs and responding to CRAN requests since 2020.

Abstract

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (‘genind’ class), alleles counts by populations (‘genpop’), and genome-wide SNP data (‘genlight’). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Installation

You can install adegenet from CRAN in R via

install.packages("adegenet")

If you want to use the in-development version of adegenet, you can install it from my R-universe:

options(repos = c(
    zkamvar = 'https://zkamvar.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'))
install.packages("adegenet")

Getting Help

You can get help for adegenet by registering for the forum at

https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

Posted on:
January 1, 0001
Length:
1 minute read, 187 words
Categories:
R package
Tags:
adegenet R population genetics
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