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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "BreedingExperiment" in publications use:'
type: software
license: MIT
title: 'BreedingExperiment: Container and Relationship Matrices for Breeding and Quantitative
  Genomics'
version: 0.99.4
identifiers:
- type: doi
  value: 10.32614/CRAN.package.BreedingExperiment
abstract: 'Provides the BreedingExperiment class, a container that keeps marker genotypes,
  phenotypes, pedigree and marker coordinates together in one object, extending RangedSummarizedExperiment
  so that markers are addressable as genomic ranges. Relationship matrices central
  to quantitative genetics are computed as methods on the container: the pedigree
  numerator relationship matrix of Henderson (1976) <https://doi.org/10.2307/2529339>,
  the genomic relationship matrix of VanRaden (2008) <https://doi.org/10.3168/jds.2007-0980>,
  the dominance relationship matrix of Vitezica, Varona and Legarra (2013) <https://doi.org/10.1534/genetics.113.155176>,
  and the single-step matrix combining pedigree and genomic information of Legarra,
  Aguilar and Misztal (2009) <https://doi.org/10.3168/jds.2009-2061> and Christensen
  and Lund (2010) <https://doi.org/10.1186/1297-9686-42-2>, which allows genotyped
  and ungenotyped individuals to be analysed together as in Aguilar and others (2010)
  <https://doi.org/10.3168/jds.2009-2730>. Marker quality control, imputation, inbreeding
  coefficients and allele frequency summaries are included.'
authors:
- family-names: Farooqi
  given-names: Muhammad
  email: mqfarooqi@gmail.com
  orcid: https://orcid.org/0000-0003-4918-9791
preferred-citation:
  type: manual
  title: 'BreedingExperiment: Container and Relationship Matrices for Breeding and
    Quantitative Genomics'
  authors:
  - family-names: Farooqi
    given-names: Muhammad
    orcid: https://orcid.org/0000-0003-4918-9791
    email: mqfarooqi@gmail.com
  year: '2026'
  notes: R package version 0.99.4
  url: https://github.com/mqfarooqi1/BreedingExperiment
repository: https://mqfarooqi1.r-universe.dev
repository-code: https://github.com/mqfarooqi1/BreedingExperiment
commit: c9e013ff73c2fe2b88ae22b5c0f6868393422a43
url: https://mqfarooqi1.github.io/BreedingExperiment/
date-released: '2026-09-04'
contact:
- family-names: Farooqi
  given-names: Muhammad
  email: mqfarooqi@gmail.com
  orcid: https://orcid.org/0000-0003-4918-9791