Package: polyRAD
Version: 1.6
Date: 2022-02-14
Title: Genotype Calling with Uncertainty from Sequencing Data in
        Polyploids and Diploids
Authors@R: c(person("Lindsay V.", "Clark", email = "lvclark@illinois.edu",
                    role = c("aut", "cre"), 
                    comment = c(ORCID = "0000-0002-3881-9252")),
             person("U.S. National Science Foundation", role = "fnd"))
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
  U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Depends: R (>= 3.5.0), methods
Imports: fastmatch, pcaMethods, Rcpp, stringi
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
        VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
        BiocGenerics, knitr, rmarkdown, GenomicFeatures, ggplot2,
        adegenet
LinkingTo: Rcpp
VignetteBuilder: knitr, rmarkdown
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction 
  site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
  probability estimates of genotypes in polyploids or diploids.  The genotype 
  probabilities, posterior mean genotypes, or most probable genotypes can then
  be exported for downstream analysis.  'polyRAD' is described by Clark et al.
  (2019) <doi:10.1534/g3.118.200913>.  A variant calling pipeline for highly
  duplicated genomes is also included and is described by Clark et al. (2020)
  <doi:10.1101/2020.01.11.902890>.
License: GPL (>= 2)
URL: https://github.com/lvclark/polyRAD
NeedsCompilation: yes
Packaged: 2022-02-15 20:14:47 UTC; lvclark
Repository: CRAN
Date/Publication: 2022-02-15 21:30:02 UTC
Built: R 4.0.5; x86_64-w64-mingw32; 2022-04-17 20:53:47 UTC; windows
Archs: i386, x64
