Exploratory Analysis of Genetic and Genomic Data
Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie-
    Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne
    Cori, Federico Calboli
pegas, hierfstat, akima, maps, splancs, adehabitat, tripack,
testthat
utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2,
seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1),
vegan
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.
adegenet.package.R datasets.R orthobasis.R classes.R
constructors.R accessors.R basicMethods.R handling.R auxil.R
minorAllele.R setAs.R SNPbin.R strataMethods.R
hierarchyMethods.R glHandle.R glFunctions.R glSim.R
find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R
chooseCN.R genind2genpop.R loadingplot.R sequences.R
gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R
coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R
xvalDapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R
export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R
simOutbreak.R mutations.R snpposi.R snpzip.R pairDist.R
servers.R zzz.R