Package: dartR
Type: Package
Title: Importing and Analysing SNP and Silicodart Data Generated by
        Genome-Wide Restriction Fragment Analysis
Version: 1.9.9.1
Date: 2021-05-28
Authors@R: c(
            person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), 
            person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"),
            person("Jose L.", "Mijangos", email="bernd.gruber@canberra.edu.au", role=c("aut")), 
            person("Peter J.", "Unmack", email="peter.mail2@unmack.net", role="ctb"),
            person("Oliver", "Berry", email="oliver.berry@csiro.au", role="ctb" ),
            person("Lindsay V.", "Clark", email="lvclark@illinois.edu", role="ctb"),
            person("Floriaan", "Devloo-Delva",email="Floriaan.Devloo-Delva@csiro.au", role="ctb"))
Description: Functions are provided that facilitate the import and analysis of
    SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
    by DarT (Diversity Arrays Technology). However, once SNP or related fragment
    presence/absence data from any source is imported into a genlight object many
    of the functions can be used. Functions are available for input and output of
    SNP and silicodart data, for reporting on and filtering on various criteria
    (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
    Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
    are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
    between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2
biocViews:
Imports: stats, methods, utils, plyr, tidyr, MASS, stringr, ape, vegan,
        SNPRelate, StAMPP, sp, PopGenReport, hierfstat, robustbase,
        gridExtra, HardyWeinberg, foreach, dplyr, crayon, devtools
Suggests: knitr, rmarkdown, rgl, parallel, doParallel, data.table,
        reshape2, pca3d, dismo, pegas, directlabels, rgdal,
        leaflet.minicharts, leaflet, rrBLUP, poppr, Rcpp, igraph,
        qvalue, gdistance, seqinr, pheatmap, RColorBrewer, gplots,
        vcfR, mmod, plotly, ggthemes, ggrepel, raster
License: GPL-2
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-05-28 10:35:24 UTC; s425824
Author: Bernd Gruber [aut, cre],
  Arthur Georges [aut],
  Jose L. Mijangos [aut],
  Peter J. Unmack [ctb],
  Oliver Berry [ctb],
  Lindsay V. Clark [ctb],
  Floriaan Devloo-Delva [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2021-05-28 17:10:05 UTC
Built: R 4.1.0; ; 2021-06-03 15:47:28 UTC; unix
