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: 2.1.0
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, tripack, testthat, poppr
Published: 2017-10-12
Author: 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
Maintainer: Thibaut Jombart <thibautjombart 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: Genetics
CRAN checks: adegenet results

Downloads:

Reference manual: adegenet.pdf
Package source: adegenet_2.1.0.tar.gz
Windows binaries: r-devel: adegenet_2.1.0.zip, r-release: adegenet_2.1.0.zip, r-oldrel: adegenet_2.1.0.zip
OS X El Capitan binaries: r-release: adegenet_2.1.0.tgz
OS X Mavericks binaries: r-oldrel: adegenet_2.1.0.tgz
Old sources: adegenet archive

Reverse dependencies:

Reverse depends: dartR, mmod, pegas, PopGenReport, poppr, strataG
Reverse imports: adephylo, AFLPsim, apex, hierfstat, outbreaker, rmetasim, skeleSim, StAMPP, treespace
Reverse suggests: EcoGenetics, HWxtest, memgene, polysat, vcfR

Linking:

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