adegenet (2.1.0)

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Exploratory Analysis of Genetic and Genomic Data.

https://github.com/thibautjombart/adegenet
http://cran.r-project.org/web/packages/adegenet

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.

Maintainer: Thibaut Jombart
Author(s): Thibaut Jombart, Zhian N. Kamvar, Caitlin Collins, Roman Lustrik, Marie- Pauline Beugin, Brian J. Knaus, Peter Solymos, Vladimir Mikryukov, Klaus Schliep, Tiago Mai, Libor Morkovsky, Ismail Ahmed, Anne Cori, Federico Calboli, RJ Ewing

License: GPL (>= 2)

Uses: ade4, ape, boot, dplyr, ggplot2, igraph, MASS, reshape2, seqinr, shiny, spdep, vegan, akima, hierfstat, maps, splancs, tripack, pegas, testthat, poppr
Reverse depends: adephylo, coalescentMCMC, dartR, epibase, mmod, outbreaker, pegas, PopGenReport, poppr, StAMPP, strataG
Reverse suggests: EcoGenetics, hierfstat, HWxtest, polysat, readGenalex, vcfR

Released about 1 month ago.


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Related packages: Biodem, GenABEL, HardyWeinberg, LDheatmap, SNPmaxsel, bqtl, gap, genetics, hapassoc, haplo.ccs, haplo.stats, hierfstat, hwde, ibdreg, luca, ouch, pbatR, qtl, rmetasim, seqinr(20 best matches, based on common tags.)


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