# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "BIGr" in publications use:'
type: software
license: Apache-2.0
title: 'BIGr: Breeding Insight Genomics Functions for Polyploid and Diploid Species'
version: 0.7.2
doi: 10.1002/tpg2.70067
identifiers:
- type: doi
  value: 10.32614/CRAN.package.BIGr
abstract: 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) <https://doi.org/10.2527/tas2016.0003>, and the 'updog' output format, see
  Gerard et al. (2018) <https://doi.org/10.1534/genetics.118.301468>.
authors:
- family-names: Sandercock
  given-names: Alexander M.
  email: sandercock.alex@gmail.com
- family-names: Taniguti
  given-names: Cristiane
- family-names: Chinchilla-Vargas
  given-names: Josue
preferred-citation:
  type: article
  title: 'BIGapp: A user-friendly genomic tool kit identified quantitative trait loci
    for creeping rootedness in alfalfa (Medicago sativa L.)'
  authors:
  - family-names: Sandercock
    given-names: Alexander M.
    email: sandercock.alex@gmail.com
  - family-names: Peel
    given-names: Michael D.
  - family-names: Taniguti
    given-names: Cristiane H.
  - family-names: Chinchilla-Vargas
    given-names: Josué
  - family-names: Chen
    given-names: Shufen
  - family-names: Sapkota
    given-names: Manoj
  - family-names: Lin
    given-names: Meng
  - family-names: Zhao
    given-names: Dongyan
  - family-names: Ackerman
    given-names: Arlyn J.
  - family-names: Basnet
    given-names: Bhoja R.
  - family-names: Beil
    given-names: Craig T.
  - family-names: Sheehan
    given-names: Moira J.
  journal: The Plant Genome
  volume: '18'
  issue: '3'
  doi: 10.1002/tpg2.70067
  year: '2025'
  start: e70067
repository: https://breeding-insight.r-universe.dev
repository-code: https://github.com/Breeding-Insight/BIGr
commit: 12798c2f6dc9da58e41a783f7f01fba1d85989ad
url: https://github.com/Breeding-Insight/BIGr
date-released: '2026-05-18'
contact:
- family-names: Sandercock
  given-names: Alexander M.
  email: sandercock.alex@gmail.com
references:
- type: manual
  title: 'BIGr: Breeding Insight Genomics functions for polyploid and diploid species'
  authors:
  - family-names: Sandercock
    given-names: Alexander M.
    email: sandercock.alex@gmail.com
  - family-names: Taniguti
    given-names: Cristiane
  - family-names: Chinchilla-Vargas
    given-names: Josue
  - family-names: Chen
    given-names: Shufen
  - family-names: Sapkota
    given-names: Manoj
  - family-names: Lin
    given-names: Meng
  - family-names: Zhao
    given-names: Dongyan
  - family-names: University
    given-names: Cornell
  year: '2025'
  notes: R package version 0.6.2
  url: https://github.com/Breeding-Insight/BIGr