Exploratory Analysis of Genetic and Genomic Data

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.

adegenet: a R Package for the Multivariate Analysis of Genetic Markers

This wiki is dedicated to the development of adegenet. It is relevant for developers of the package, developers of other packages depending on adegenet, and for users who want to be using the latest features as well.

The adegenet website is available at http://adegenet.r-forge.r-project.org/.

The following sections are available:


Reference manual

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2.0.1 by Thibaut Jombart, 2 years ago


Browse source code at https://github.com/cran/adegenet

Authors: Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie- Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli

Documentation:   PDF Manual  

Task views: Statistical Genetics

GPL (>= 2) license

Imports utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, spdep, boot, reshape2, dplyr, vegan

Depends on methods, ade4

Suggests pegas, hierfstat, akima, maps, splancs, adehabitat, tripack, testthat

Imported by AFLPsim, StAMPP, adephylo, apex, geomedb, hierfstat, outbreaker, rmetasim, skeleSim, treespace.

Depended on by PopGenReport, dartR, mmod, pegas, poppr, strataG.

Suggested by EcoGenetics, HWxtest, memgene, polysat, vcfR.

See at CRAN