BreastSubtypeR
This is the development version of BreastSubtypeR; for the stable release version, see BreastSubtypeR.
Cohort-aware methods for intrinsic molecular subtyping of breast cancer
Bioconductor version: Development (3.24)
BreastSubtypeR provides an assumption-aware, multi-method framework for intrinsic molecular subtyping of breast cancer. The package harmonizes several published nearest-centroid (NC) and single-sample predictor (SSP) classifiers, supplies method-specific preprocessing and robust probe-to-gene mapping, and implements a cohort-aware AUTO mode that selectively enables classifiers compatible with the cohort composition. A local Shiny app (iBreastSubtypeR) is included for interactive analyses and to support users without programming experience.
Author: Qiao Yang [aut, cre]
, Emmanouil G. Sifakis [aut]
Maintainer: Qiao Yang <yq.kiuo at gmail.com>
citation("BreastSubtypeR")):
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("BreastSubtypeR")
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("BreastSubtypeR")| BreastSubtypeR: Introduction and Workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, Preprocessing, RNASeq, Software, Visualization |
| Version | 1.5.1 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang, stringr, withr, edgeR, ComplexHeatmap, impute(>= 1.80.0), data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>= 0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8), SummarizedExperiment, utils |
| System Requirements | |
| URL | https://doi.org/10.18129/B9.bioc.BreastSubtypeR https://github.com/yqkiuo/BreastSubtypeR https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR |
| Bug Reports | https://github.com/yqkiuo/BreastSubtypeR/issues |
See More
| Suggests | lifecycle, tidyverse, shiny (>= 1.9.1), bslib (>= 0.8.0), BiocStyle, knitr, rmarkdown, testthat |
| 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 | BreastSubtypeR_1.5.1.tar.gz |
| Windows Binary (x86_64) | BreastSubtypeR_1.5.1.zip |
| macOS Binary (big-sur-x86_64) | BreastSubtypeR_1.5.1.tgz |
| macOS Binary (sonoma-arm64) | BreastSubtypeR_1.5.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BreastSubtypeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BreastSubtypeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/BreastSubtypeR/ |
| Package Short Url | https://bioconductor.org/packages/BreastSubtypeR/ |
| Package Downloads Report | Download Stats |