Package: BIGr
Title: Breeding Insight Genomics Functions for Polyploid and Diploid
        Species
Version: 0.7.2
Authors@R: c(person(given='Alexander M.',
                    family='Sandercock',
                    email='sandercock.alex@gmail.com',
                    role=c('cre','aut')),
             person(given='Cristiane',
                    family='Taniguti',
                    role = 'aut'),
             person(given='Josue',
                    family='Chinchilla-Vargas',
                    role='aut'),
             person(given='Shufen',
                    family='Chen',
                    role='ctb'),
             person(given='Manoj',
                    family='Sapkota',
                    role='ctb'),
             person(given='Meng',
                    family='Lin',
                    role='ctb'),
             person(given='Dongyan',
                    family='Zhao',
                    role='ctb'),
             person('University', "of Florida",
                    role=c('cph'), 
                    comment = "Breeding Insight"))
Maintainer: Alexander M. Sandercock <sandercock.alex@gmail.com>
Description: Functions developed within Breeding Insight to analyze
        diploid and polyploid breeding and genetic data. 'BIGr'
        provides the ability to filter variant call format (VCF) files,
        extract single nucleotide polymorphisms (SNPs) from diversity
        arrays technology missing allele discovery count (DArT MADC)
        files, and manipulate genotype data for both diploid and
        polyploid species. It also serves as the core dependency for
        the 'BIGapp' 'Shiny' app, which provides a user-friendly
        interface for performing routine genotype analysis tasks such
        as dosage calling, filtering, principal component analysis
        (PCA), genome-wide association studies (GWAS), and genomic
        prediction. For more details about the included 'breedTools'
        functions, see Funkhouser et al. (2017)
        <doi:10.2527/tas2016.0003>, and the 'updog' output format, see
        Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
License: Apache License (>= 2)
URL: https://github.com/Breeding-Insight/BIGr
BugReports: https://github.com/Breeding-Insight/BIGr/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.4.0)
biocViews:
Imports: parallel, dplyr, Rdpack (>= 0.7), readr (>= 2.1.5), reshape2
        (>= 1.4.4), rlang, tidyr (>= 1.3.1), vcfR (>= 1.15.0),
        Rsamtools, Biostrings, pwalign, janitor, quadprog, tibble,
        stringr, data.table
Suggests: covr, ggplot2, spelling, rmdformats, knitr (>= 1.10),
        rmarkdown, polyRAD, testthat (>= 3.0.0)
RdMacros: Rdpack
Config/pak/sysreqs: libbz2-dev libicu-dev liblzma-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://breeding-insight.r-universe.dev
Date/Publication: 2026-05-18 12:03:32 UTC
RemoteUrl: https://github.com/breeding-insight/bigr
RemoteRef: HEAD
RemoteSha: 12798c2f6dc9da58e41a783f7f01fba1d85989ad
NeedsCompilation: no
Packaged: 2026-09-21 12:04:07 UTC; root
Author: Alexander M. Sandercock [cre, aut],
  Cristiane Taniguti [aut],
  Josue Chinchilla-Vargas [aut],
  Shufen Chen [ctb],
  Manoj Sapkota [ctb],
  Meng Lin [ctb],
  Dongyan Zhao [ctb],
  University of Florida [cph] (Breeding Insight)