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# 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 "PCAPAM50" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'PCAPAM50: Enhanced ''PAM50'' Subtyping of Breast Cancer'
version: 1.0.2
doi: 10.1038/s41598-019-44339-4
identifiers:
- type: doi
  value: 10.32614/CRAN.package.PCAPAM50
abstract: Accurate classification of breast cancer tumors based on gene expression
  data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier,
  which uses 50 gene centroid correlation distances to classify tumors, faces challenges
  with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50'
  package leverages principal component analysis and iterative 'PAM50' calls to create
  a gene expression-based ER-balanced subset for gene centering, avoiding the use
  of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.
authors:
- family-names: Raj-Kumar
  given-names: Praveen-Kumar
  email: p.rajkumar@wriwindber.org
- family-names: Chen
  given-names: Boyi
- family-names: Hu
  given-names: Ming-Wen
- family-names: Hohenstein
  given-names: Tyler
- family-names: Liu
  given-names: Jianfang
- family-names: Shriver
  given-names: Craig D.
- family-names: Lin
  given-names: Xiaoying
- family-names: Hu
  given-names: Hai
preferred-citation:
  type: article
  title: PCA-PAM50 improves consistency between breast cancer intrinsic and clinical
    subtyping reclassifying a subset of luminal A tumors as luminal B
  authors:
  - family-names: Raj-Kumar
    given-names: Praveen-Kumar
    email: p.rajkumar@wriwindber.org
  - family-names: Liu
    given-names: Jianfang
  - family-names: Hooke
    given-names: Jeffrey A.
  - family-names: Kovatich
    given-names: Albert J.
  - family-names: Kvecher
    given-names: Leonid
  - family-names: Shriver
    given-names: Craig D.
  - family-names: Hu
    given-names: Hai
  journal: Scientific Reports
  year: '2019'
  volume: '9'
  issue: '1'
  publisher:
    name: Nature Publishing Group UK London
  doi: 10.1038/s41598-019-44339-4
  start: '7956'
repository: https://CRAN.R-project.org/package=PCAPAM50
date-released: '2024-11-24'
contact:
- family-names: Raj-Kumar
  given-names: Praveen-Kumar
  email: p.rajkumar@wriwindber.org
references:
- type: article
  title: Supervised risk predictor of breast cancer based on intrinsic subtypes
  authors:
  - family-names: Parker
    given-names: Joel S.
  - family-names: Mullins
    given-names: Michael
  - family-names: Cheang
    given-names: Maggie CU
  - family-names: Leung
    given-names: Samuel
  - family-names: Voduc
    given-names: David
  - family-names: Vickery
    given-names: Tammi
  - family-names: Davies
    given-names: Sherri
  - family-names: Fauron
    given-names: Christiane
  - family-names: He
    given-names: Xiaping
  - family-names: Hu
    given-names: Zhiyuan
  - name: et al.
  journal: Journal of Clinical Oncology
  year: '2009'
  volume: '27'
  issue: '8'
  publisher:
    name: American Society of Clinical Oncology
  doi: 10.1200/JCO.2008.18.1370
  start: '1160'
  end: '1167'