thyroidBRS
This is the development version of thyroidBRS; to use it, please install the devel version of Bioconductor.
BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma
Bioconductor version: Development (3.24)
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.
Author: Camila Barrios-Cervantes [aut, cph] 
, Daniel Pérez-Calixto [aut, cph] , Hugo Tovar [aut, cre, cph] , Instituto Nacional de Medicina Genómica [fnd] (ROR: <https://ror.org/01qjckx08>, project: INMEGEN-2026-14 (Proyecto 81))
Maintainer: Hugo Tovar <hatovar at inmegen.gob.mx>
citation("thyroidBRS")):Camila Barrios-Cervantes, Daniel Pérez-Calixto, Hugo Tovar. thyroidBRS: BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma. doi:10.18129/B9.bioc.thyroidBRS, R package version 0.99.7, https://bioconductor.org/packages/thyroidBRS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("thyroidBRS")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("thyroidBRS")| Introduction to thyroidBRS | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Classification, DriverMutation, GeneExpression, Microarray, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5) |
| Imports | SummarizedExperiment, methods, stats |
| System Requirements | |
| URL | https://github.com/camilasauria/thyroidBRS |
| Bug Reports | https://github.com/camilasauria/thyroidBRS/issues |
See More
| Suggests | Biobase, BiocStyle, knitr, rmarkdown, testthat (>= 3.1.5) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/thyroidBRS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/thyroidBRS |
| Package Short Url | https://bioconductor.org/packages/thyroidBRS/ |
| Package Downloads Report | Download Stats |