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 (3.23)
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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BreastSubtypeR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Classification, GeneExpression, Preprocessing, RNASeq, Software, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/BreastSubtypeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BreastSubtypeR |
| Package Short Url | https://bioconductor.org/packages/BreastSubtypeR/ |
| Package Downloads Report | Download Stats |