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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 "thyroidBRS" in publications use:'
type: software
license: MIT
title: 'thyroidBRS: BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma'
version: 0.99.7
abstract: 'Computes the BRAF-RAS Score (BRS), a 71-gene expression-based signature
  that quantifies whether a papillary thyroid carcinoma (PTC) sample resembles a BRAF-V600E-mutant
  or a RAS-mutant transcriptional profile, following Agrawal et al. (2014) <https://doi.org/10.1016/j.cell.2014.09.050>,
  Extended Experimental Procedures, section 14.1. It is a re-implementation from that
  description rather than the original code, which was never released: it reproduces
  the published classification (99.7 percent against driver-mutation status under
  cross-validation) but not the exact published score values. The original study only
  scored the subset of samples for which both exome and RNA sequencing data were available,
  since exome data was needed to define the two reference groups (but not to score
  additional samples). This package lets you fit the reference centroids from any
  cohort with known BRAF-mutant/RAS-mutant labels and then score new samples — including
  ones with expression data only — using just their gene expression. Expression can
  be supplied as a matrix, a SummarizedExperiment or an ExpressionSet.'
authors:
- family-names: Barrios-Cervantes
  given-names: Camila
  email: paulacamilabarrioscervantes@gmail.com
  orcid: https://orcid.org/0009-0006-9971-790X
- family-names: Pérez-Calixto
  given-names: Daniel
  email: daniel_perez@ciencias.unam.mx
  orcid: https://orcid.org/0009-0004-3988-1260
- family-names: Tovar
  given-names: Hugo
  email: hatovar@inmegen.gob.mx
  orcid: https://orcid.org/0000-0002-8360-6133
preferred-citation:
  type: manual
  title: 'thyroidBRS: BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma'
  authors:
  - family-names: Barrios-Cervantes
    given-names: Camila
    email: paulacamilabarrioscervantes@gmail.com
    orcid: https://orcid.org/0009-0006-9971-790X
  - family-names: Pérez-Calixto
    given-names: Daniel
    email: daniel_perez@ciencias.unam.mx
    orcid: https://orcid.org/0009-0004-3988-1260
  - family-names: Tovar
    given-names: Hugo
    email: hatovar@inmegen.gob.mx
    orcid: https://orcid.org/0000-0002-8360-6133
  year: '2026'
  notes: R package version 0.99.7
  url: https://github.com/camilasauria/thyroidBRS
repository: https://bioc.r-universe.dev
repository-code: https://github.com/camilasauria/thyroidBRS
commit: a6750a1885f3ba7c784b3465047f3d0ed93787d0
url: https://github.com/camilasauria/thyroidBRS
date-released: '2026-10-09'
contact:
- family-names: Tovar
  given-names: Hugo
  email: hatovar@inmegen.gob.mx
  orcid: https://orcid.org/0000-0002-8360-6133
references:
- type: article
  title: Integrated Genomic Characterization of Papillary Thyroid Carcinoma
  authors:
  - name: The Cancer Genome Atlas Research Network
  journal: Cell
  year: '2014'
  volume: '159'
  issue: '3'
  doi: 10.1016/j.cell.2014.09.050
  start: '676'
  end: '690'