Package: BreastSubtypeR 1.5.1

Qiao Yang

BreastSubtypeR: Cohort-aware methods for intrinsic molecular subtyping of breast cancer

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.

Authors:Qiao Yang [aut, cre], Emmanouil G. Sifakis [aut]

BreastSubtypeR_1.5.1.tar.gz
BreastSubtypeR_1.5.1.zip(r-4.7)BreastSubtypeR_1.5.1.zip(r-4.6)BreastSubtypeR_1.5.1.zip(r-4.5)
BreastSubtypeR_1.5.1.tgz(r-4.6-any)BreastSubtypeR_1.5.1.tgz(r-4.5-any)
BreastSubtypeR_1.5.1.tar.gz(r-4.7-any)BreastSubtypeR_1.5.1.tar.gz(r-4.6-any)
BreastSubtypeR_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BreastSubtypeR/json (API)

# Install 'BreastSubtypeR' in R:

install.packages('BreastSubtypeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yqkiuo/breastsubtyper/issues

Datasets:

AIMSmodel - AIMSmodel: Model object for AIMS
BreastSubtypeRobj - BreastSubtypeRobj: Resources for NC-based methods
Gene.ID.ann - Gene.ID.ann: Gene annotation table
OSLO2EMIT0obj - OSLO2EMIT0obj: Example dataset
sspbc.models - Sspbc.models: Short names for 11 SSPBC predictors
sspbc.models.fullname - Sspbc.models.fullname: Full names for 11 SSPBC predictors
TCGABRCAobj - TCGABRCAobj: Example dataset

On BioConductor:BreastSubtypeR-1.5.0(bioc 3.24)BreastSubtypeR-1.4.0(bioc 3.23)

rnaseq software geneexpression classification preprocessing visualization

5.56 score 6 stars 12 scripts 15 exports 71 dependencies

Last updated from:435e0e17f1. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	205
linux-devel-x86_64	OK	366
source / vignettes	OK	290
linux-release-x86_64	OK	329
macos-release-arm64	OK	214
macos-oldrel-arm64	OK	152
windows-devel	OK	257
windows-release	OK	232
windows-oldrel	OK	241
wasm-release	OK	149

Exports:BS_AIMS BS_cIHC BS_cIHC.itr BS_Multi BS_parker BS_PCAPAM50 BS_ssBC BS_sspbc iBreastSubtypeR Mapping Vis_boxplot Vis_heatmap Vis_Multi Vis_PCA Vis_pie

Dependencies:abind Biobase BiocGenerics circlize class cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon data.table DelayedArray digest doParallel dplyr e1071 edgeR farver foreach generics GenomicRanges GetoptLong ggplot2 ggrepel GlobalOptions glue gtable impute IRanges isoband iterators labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats pillar pkgconfig png proxy R6 RColorBrewer Rcpp rjson rlang S4Arrays S4Vectors S7 scales Seqinfo shape SparseArray statmod stringi stringr SummarizedExperiment tibble tidyselect utf8 vctrs viridisLite withr XVector

BreastSubtypeR: Introduction and Workflow

Rendered fromBreastSubtypeR.Rmdusingknitr::rmarkdown

Last update: 2025-11-23
Started: 2024-12-17

Help page	Topics
AIMSmodel: Model object for AIMS	AIMSmodel
BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research	BreastSubtypeR-package BreastSubtypeR
BreastSubtypeRobj: Resources for NC-based methods	BreastSubtypeRobj
AIMS Intrinsic Subtyping (BS_AIMS)	BS_AIMS
Conventional IHC Intrinsic Subtyping (BS_cIHC)	BS_cIHC
Iterative Conventional IHC Intrinsic Subtyping (BS_cIHC.itr)	BS_cIHC.itr
Intrinsic Subtyping with Multiple Approaches (BS_Multi)	BS_Multi
Original Parker Intrinsic Subtyping (BS_parker)	BS_parker
PCA-PAM50 Intrinsic Subtyping (BS_PCAPAM50)	BS_PCAPAM50
Subgroup-Specific Gene-Centering Intrinsic Subtyping (BS_ssBC)	BS_ssBC
Intrinsic Subtyping using SSPBC (BS_sspbc)	BS_sspbc
Gene.ID.ann: Gene annotation table	Gene.ID.ann
Launch the iBreastSubtypeR Shiny app	iBreastSubtypeR
Gene ID Mapping	Mapping
OSLO2EMIT0obj: Example dataset (OSLO2-EMIT0 cohort subset)	OSLO2EMIT0obj
sspbc.models: Short names for 11 SSPBC predictors	sspbc.models
sspbc.models.fullname: Full names for 11 SSPBC predictors	sspbc.models.fullname
TCGABRCAobj: Example dataset (TCGA-BRCA subset)	TCGABRCAobj
Boxplot of Correlation per Subtype	Vis_boxplot
Heatmap Visualization of Gene Expression by Subtype	Vis_heatmap
Multi-Method Subtype Heatmap Visualization	Vis_Multi
PCA Plot Visualization of Gene Expression by Subtype	Vis_PCA
Pie Chart Visualization of Subtype Distribution	Vis_pie

Package: BreastSubtypeR 1.5.1

BreastSubtypeR: Cohort-aware methods for intrinsic molecular subtyping of breast cancer

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Help Manual

Usage by other packages (reverse dependencies)