Package: GBScleanR
Type: Package
Title: Error correction tool for noisy genotyping by sequencing (GBS)
        data
Version: 2.4.4
Date: 2025-11-30
Authors@R: person("Tomoyuki", "Furuta", 
           email = "f.tomoyuki@okayama-u.ac.jp",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0869-6626"))
Description: GBScleanR is a package for quality check, filtering, and
        error correction of genotype data derived from next generation
        sequcener (NGS) based genotyping platforms. GBScleanR takes
        Variant Call Format (VCF) file as input. The main function of
        this package is `estGeno()` which estimates the true genotypes
        of samples from given read counts for genotype markers using a
        hidden Markov model with incorporating uneven observation ratio
        of allelic reads. This implementation gives robust genotype
        estimation even in noisy genotype data usually observed in
        Genotyping-By-Sequnencing (GBS) and similar methods, e.g.
        RADseq. The current implementation accepts genotype data of a
        diploid population at any generation of multi-parental cross,
        e.g. biparental F2 from inbred parents, biparental F2 from
        outbred parents, and 8-way recombinant inbred lines (8-way
        RILs) which can be refered to as MAGIC population.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LinkingTo: Rcpp, RcppParallel
SystemRequirements: GNU make, C++11
Depends: SeqArray
Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp,
        RcppParallel, gdsfmt
Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: GeneticVariability, SNP, Genetics, HiddenMarkovModel,
        Sequencing, QualityControl
BugReports: https://github.com/tomoyukif/GBScleanR/issues
URL: https://github.com/tomoyukif/GBScleanR
Config/testthat/edition: 3
Config/pak/sysreqs: make libicu-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-30 03:33:12 UTC
RemoteUrl: https://github.com/bioc/GBScleanR
RemoteRef: RELEASE_3_22
RemoteSha: 84bfa8a1cbfec19fab086ace2bac2595246e3bb5
NeedsCompilation: yes
Packaged: 2025-12-01 04:38:54 UTC; root
Author: Tomoyuki Furuta [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0869-6626>)
Maintainer: Tomoyuki Furuta <f.tomoyuki@okayama-u.ac.jp>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-12-01 04:41:32 UTC; windows
Archs: x64
