Package: thyroidBRS
Title: BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma
Version: 0.99.9
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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-23 20:08:13 UTC
RemoteUrl: https://github.com/bioc/thyroidBRS
RemoteRef: HEAD
RemoteSha: de985ce145ca519a4cc5c136616bd1abc8447b21
NeedsCompilation: no
Packaged: 2026-10-23 22:29:39 UTC; root
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>