Package: polyRAD
Version: 2.0.1
Date: 2026-03-21
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, txdbmaker, polymapR, BSgenome
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
Config/pak/sysreqs: libicu-dev
Repository: https://lvclark.r-universe.dev
Date/Publication: 2026-03-22 00:34:31 UTC
RemoteUrl: https://github.com/lvclark/polyRAD
RemoteRef: HEAD
RemoteSha: 4408d65bfd59b2d643d26eb869339348be61b13e
NeedsCompilation: yes
Packaged: 2026-06-24 11:00:34 UTC; root