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.

Documentation

Manual: adegenet.pdf
Vignette: None available.

Maintainer: Thibaut Jombart <thibautjombart at gmail.com>

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

Install package and any missing dependencies by running this line in your R console:

install.packages("adegenet")

Depends R (>= 2.14), methods, ade4
Imports utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, spdep, boot, reshape2, dplyr(>=0.4.1), vegan
Suggests pegas, hierfstat, akima, maps, splancs, adehabitat, tripack, testthat
Enhances
Linking to
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depends
mmod, pegas, PopGenReport, poppr, strataG
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imports
adephylo, AFLPsim, apex, hierfstat, outbreaker, rmetasim, skeleSim, StAMPP, treescape, treespace
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suggests
EcoGenetics, HWxtest, memgene, polysat, vcfR
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enhances
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linking to

Package adegenet
Materials
URL http://adegenet.r-forge.r-project.org/
Task Views Genetics
Version 2.0.1
Published 2016-02-15
License GPL (>= 2)
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks adegenet check results
Package source adegenet_2.0.1.tar.gz