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 [aut], Zhian N. Kamvar [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 [ctb], Lindsay V. Clark [ctb], Pavel Dimens [ctb]
Maintainer:	Zhian N. Kamvar <zkamvar at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://github.com/thibautjombart/adegenet
NeedsCompilation:	yes
Citation:	adegenet citation info
Materials:	README ChangeLog
In views:	Epidemiology
CRAN checks:	adegenet results

Documentation:

Reference manual:

adegenet.pdf

Downloads:

Package source:	adegenet_2.1.10.tar.gz
Windows binaries:	r-devel: adegenet_2.1.10.zip, r-release: adegenet_2.1.10.zip, r-oldrel: adegenet_2.1.10.zip
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.data, dartR.popgen, dartR.sexlinked, dartR.sim, dartR.spatial, mmod, PopGenReport, poppr
Reverse imports:	adephylo, AlleleShift, apex, DA, graph4lg, hierfstat, snpAIMeR, SNPfiltR, StAMPP, treespace
Reverse suggests:	coreCollection, memgene, outbreaker2, pegas, polyRAD, polysat, quiddich, RAINBOWR, sequoia, vcfR, wingen

Linking:

Please use the canonical form https://CRAN.R-project.org/package=adegenet to link to this page.