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: 2.0.1
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
Published: 2016-02-15
Author: Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie- Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli
Maintainer: Thibaut Jombart <thibautjombart at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://adegenet.r-forge.r-project.org/
NeedsCompilation: yes
Citation: adegenet citation info
Materials: README ChangeLog
In views: Genetics
CRAN checks: adegenet results

Downloads:

Reference manual: adegenet.pdf
Package source: adegenet_2.0.1.tar.gz
Windows binaries: r-devel: adegenet_2.0.1.zip, r-release: adegenet_2.0.1.zip, r-oldrel: adegenet_2.0.1.zip
OS X Mavericks binaries: r-release: adegenet_2.0.1.tgz, r-oldrel: adegenet_2.0.1.tgz
Old sources: adegenet archive

Reverse dependencies:

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

Linking:

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