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BreastSubtypeR
This is thereleased version of BreastSubtypeR; for the devel version, seeBreastSubtypeR.
Cohort-aware methods for intrinsic molecular subtyping of breast cancer
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0002-4098-3246, Emmanouil G. Sifakis [aut] ORCID: 0000-0001-9919-4471
Maintainer: Qiao Yang <yq.kiuo at gmail.com>
citation("BreastSubtypeR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("BreastSubtypeR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.2.0 |
| 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.BreastSubtypeRhttps://github.com/yqkiuo/BreastSubtypeRhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | BreastSubtypeR_1.2.0.tar.gz |
| Windows Binary (x86_64) | BreastSubtypeR_1.2.0.zip |
| macOS Binary (x86_64) | BreastSubtypeR_1.2.0.tgz |
| macOS Binary (arm64) | BreastSubtypeR_1.2.0.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 |