Package: thyroidBRS
Title: BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma
Version: 0.99.7
Authors@R: c(
    person("Camila", "Barrios-Cervantes",
           email = "paulacamilabarrioscervantes@gmail.com",
           role = c("aut", "cph"),
           comment = c(ORCID = "0009-0006-9971-790X")),
    person("Daniel", "Pérez-Calixto",
           email = "daniel_perez@ciencias.unam.mx",
           role = c("aut", "cph"),
           comment = c(ORCID = "0009-0004-3988-1260")),
    person("Hugo", "Tovar",
           email = "hatovar@inmegen.gob.mx",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8360-6133")),
    person("Instituto Nacional de Medicina Genómica", role = "fnd",
           comment = c(ROR = "https://ror.org/01qjckx08",
                       project = "INMEGEN-2026-14 (Proyecto 81)")))
Description: 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) <doi: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.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: Software, Classification, DriverMutation, GeneExpression,
        Transcriptomics, RNASeq, Microarray, Sequencing,
        BiomedicalInformatics
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.5)
Imports: SummarizedExperiment, methods, stats
Suggests: Biobase, BiocStyle, knitr, rmarkdown, testthat (>= 3.1.5)
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://github.com/camilasauria/thyroidBRS
BugReports: https://github.com/camilasauria/thyroidBRS/issues
Config/roxygen2/version: 8.1.0
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/thyroidBRS
git_branch: devel
git_last_commit: a6750a1
git_last_commit_date: 2026-10-09
Repository: Bioconductor 3.24
Date/Publication: 2026-10-11
NeedsCompilation: no
Packaged: 2026-10-12 00:42:24 UTC; biocbuild
Author: Camila Barrios-Cervantes [aut, cph] (ORCID:
    <https://orcid.org/0009-0006-9971-790X>),
  Daniel Pérez-Calixto [aut, cph] (ORCID:
    <https://orcid.org/0009-0004-3988-1260>),
  Hugo Tovar [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8360-6133>),
  Instituto Nacional de Medicina Genómica [fnd] (ROR:
    <https://ror.org/01qjckx08>, project: INMEGEN-2026-14 (Proyecto
    81))
Maintainer: Hugo Tovar <hatovar@inmegen.gob.mx>
