adegenet: 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.

Version: 2.1.10
Depends: R (≥ 2.14), methods, ade4
Imports: utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, boot, reshape2, dplyr (≥ 0.4.1), vegan
Suggests: adespatial, pegas, hierfstat, maps, spdep, interp, splancs, poppr, testthat
Published: 2023-01-26
DOI: 10.32614/CRAN.package.adegenet
Author: Thibaut Jombart ORCID iD [aut], Zhian N. Kamvar ORCID iD [aut, cre], Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol ORCID iD [ctb], Lindsay V. Clark ORCID iD [ctb], Pavel Dimens ORCID iD [ctb]
Maintainer: Zhian N. Kamvar <zkamvar at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: adegenet citation info
Materials: README ChangeLog
In views: Epidemiology
CRAN checks: adegenet results


Reference manual: adegenet.pdf


Package source: adegenet_2.1.10.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): adegenet_2.1.10.tgz, r-oldrel (arm64): adegenet_2.1.10.tgz, r-release (x86_64): adegenet_2.1.10.tgz, r-oldrel (x86_64): adegenet_2.1.10.tgz
Old sources: adegenet archive

Reverse dependencies:

Reverse depends: dartR, dartR.base, dartR.captive,, dartR.popgen, dartR.sexlinked, dartR.sim, dartR.spatial, mmod, PopGenReport, poppr
Reverse imports: adephylo, AlleleShift, apex, DA, graph4lg, hierfstat, PopGenHelpR, snpAIMeR, SNPfiltR, StAMPP, treespace
Reverse suggests: coreCollection, memgene, outbreaker2, pegas, polyRAD, polysat, quiddich, RAINBOWR, sequoia, vcfR, wingen


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