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:

News

Reference manual

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install.packages("adegenet")

2.1.0 by Thibaut Jombart, a month ago


https://github.com/thibautjombart/adegenet


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


Authors: Thibaut Jombart, Zhian N. Kamvar, Caitlin Collins, Roman Lustrik, Marie- Pauline Beugin, Brian J. Knaus, Peter Solymos, Vladimir Mikryukov, Klaus Schliep, Tiago MaiƩ, Libor Morkovsky, Ismail Ahmed, Anne Cori, Federico Calboli, RJ Ewing


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, tripack, testthat, poppr


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

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

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


See at CRAN