DESCRIPTION

Package: polyRAD
Version: 2.0.0.9004
Date: 2025-03-08
Title: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Authors@R: c(person("Lindsay V.", "Clark", email = "Lindsay.Clark@seattlechildrens.org",
                    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 <Lindsay.Clark@seattlechildrens.org>
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>, and the Hind/He statistic for marker
  filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
  A variant calling pipeline for highly duplicated genomes is also included and
  is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.
License: GPL (>= 2)
URL: https://github.com/lvclark/polyRAD