# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "BreastSubtypeR" in publications use:'
type: software
license: GPL-3.0-only
title: 'BreastSubtypeR: Cohort-aware methods for intrinsic molecular subtyping of
  breast cancer'
version: 1.5.0
doi: 10.1093/nargab/lqaf131
identifiers:
- type: doi
  value: 10.32614/CRAN.package.BreastSubtypeR
- type: url
  value: https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR
abstract: BreastSubtypeR provides an assumption-aware, multi-method framework for
  intrinsic molecular subtyping of breast cancer. The package harmonizes several published
  nearest-centroid (NC) and single-sample predictor (SSP) classifiers, supplies method-specific
  preprocessing and robust probe-to-gene mapping, and implements a cohort-aware AUTO
  mode that selectively enables classifiers compatible with the cohort composition.
  A local Shiny app (iBreastSubtypeR) is included for interactive analyses and to
  support users without programming experience.
authors:
- family-names: Yang
  given-names: Qiao
  email: yq.kiuo@gmail.com
  orcid: https://orcid.org/0000-0002-4098-3246
- family-names: Sifakis
  given-names: Emmanouil G.
  email: emmanouil.sifakis@ki.se
  orcid: https://orcid.org/0000-0001-9919-4471
preferred-citation:
  type: article
  title: 'BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular
    subtyping in breast cancer research'
  authors:
  - family-names: Yang
    given-names: Qiao
    email: yq.kiuo@gmail.com
    orcid: https://orcid.org/0000-0002-4098-3246
  - family-names: Hartman
    given-names: Johan
  - family-names: Sifakis
    given-names: Emmanouil G.
    email: emmanouil.sifakis@ki.se
    orcid: https://orcid.org/0000-0001-9919-4471
  journal: NAR Genomics and Bioinformatics
  year: '2025'
  volume: '7'
  issue: '4'
  doi: 10.1093/nargab/lqaf131
  url: https://doi.org/10.1093/nargab/lqaf131
  start: lqaf131
repository: https://bioc.r-universe.dev
repository-code: https://github.com/yqkiuo/BreastSubtypeR
commit: 7bd9607c6b0050cbe5c65034a2cb93d5225376ff
url: https://doi.org/10.18129/B9.bioc.BreastSubtypeR
date-released: '2026-04-28'
contact:
- family-names: Yang
  given-names: Qiao
  email: yq.kiuo@gmail.com
  orcid: https://orcid.org/0000-0002-4098-3246
references:
- type: manual
  title: 'BreastSubtypeR: Cohort-aware methods for intrinsic molecular subtyping of
    breast cancer'
  authors:
  - family-names: Yang
    given-names: Qiao
    email: yq.kiuo@gmail.com
    orcid: https://orcid.org/0000-0002-4098-3246
  - family-names: Sifakis
    given-names: Emmanouil G.
    email: emmanouil.sifakis@ki.se
    orcid: https://orcid.org/0000-0001-9919-4471
  year: '2026'
  notes: R package version 1.5.0
  url: https://doi.org/10.18129/B9.bioc.BreastSubtypeR
  doi: 10.18129/B9.bioc.BreastSubtypeR