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)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | thyroidBRS_0.99.7.tar.gz |
| Windows Binary (x86_64) | thyroidBRS_0.99.7.zip |
| macOS Binary (big-sur-x86_64) | thyroidBRS_0.99.7.tgz |
| macOS Binary (sonoma-arm64) | thyroidBRS_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/thyroidBRS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/thyroidBRS |
| Bioc Package Browser | https://code.bioconductor.org/browse/thyroidBRS/ |
| Package Short Url | https://bioconductor.org/packages/thyroidBRS/ |
| Package Downloads Report | Download Stats |