# --------------------------------------------
# CITATION 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 "updog" in publications use:'
type: software
license: GPL-3.0-only
title: 'updog: Flexible Genotyping for Polyploids'
version: 2.1.5
doi: 10.1534/genetics.118.301468
identifiers:
- type: doi
  value: 10.32614/CRAN.package.updog
abstract: Implements empirical Bayes approaches to genotype polyploids from next generation
  sequencing data while accounting for allele bias, overdispersion, and sequencing
  error. The main functions are flexdog() and multidog(), which allow the specification
  of many different genotype distributions. Also provided are functions to simulate
  genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate
  oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes,
  oracle_cor(). These latter two functions are useful for read depth calculations.
  Run browseVignettes(package = "updog") in R for example usage. See Gerard et al.
  (2018) <https://doi.org/10.1534/genetics.118.301468> and Gerard and Ferrao (2020)
  <https://doi.org/10.1093/bioinformatics/btz852> for details on the implemented methods.
authors:
- family-names: Gerard
  given-names: David
  email: gerard.1787@gmail.com
  orcid: https://orcid.org/0000-0001-9450-5023
preferred-citation:
  type: article
  title: Genotyping Polyploids from Messy Sequencing Data
  authors:
  - family-names: Gerard
    given-names: David
    email: gerard.1787@gmail.com
    orcid: https://orcid.org/0000-0001-9450-5023
  - family-names: Ferr\~ao
    given-names: Lu\'is Felipe Ventorim
    email: lfelipe.ferrao@gmail.com
  - family-names: Garcia
    given-names: Antonio Augusto Franco
    email: aafgarci@esalq.usp.br
  - family-names: Stephens
    given-names: Matthew
    email: mstephens@uchicago.edu
  year: '2018'
  journal: Genetics
  publisher:
    name: Genetics
  volume: '210'
  issue: '3'
  issn: 0016-6731
  doi: 10.1534/genetics.118.301468
  start: '789'
  end: '807'
repository: https://polyploids.r-universe.dev
repository-code: https://github.com/dcgerard/updog
commit: 13e6a7b202d74e969f2837d2eeb136767593dc4f
url: https://github.com/dcgerard/updog/
contact:
- family-names: Gerard
  given-names: David
  email: gerard.1787@gmail.com
  orcid: https://orcid.org/0000-0001-9450-5023
references:
- type: article
  title: Priors for Genotyping Polyploids
  authors:
  - family-names: Gerard
    given-names: David
    email: gerard.1787@gmail.com
  - family-names: Ferr\~ao
    given-names: Lu\'is Felipe Ventorim
    email: lfelipe.ferrao@gmail.com
  year: '2020'
  journal: Bioinformatics
  publisher:
    name: Oxford University Press
  volume: '36'
  issue: '6'
  issn: 1367-4803
  doi: 10.1093/bioinformatics/btz852
  start: '1795'
  end: '1800'