Package: BreastSubtypeR 1.5.12

Emmanouil G. Sifakis

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], Emmanouil G. Sifakis [aut, cre]

BreastSubtypeR_1.5.12.tar.gz
BreastSubtypeR_1.5.12.zip(r-4.7-any)BreastSubtypeR_1.5.12.zip(r-4.6-any)BreastSubtypeR_1.5.12.zip(r-4.5-any)
BreastSubtypeR_1.5.12.tgz(r-4.6-any)BreastSubtypeR_1.5.12.tgz(r-4.5-any)
BreastSubtypeR_1.5.12.tar.gz(r-4.7-any)BreastSubtypeR_1.5.12.tar.gz(r-4.6-any)
BreastSubtypeR_1.5.12.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/johanhartmangroupbioteam/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-1.5.11(bioc 3.24)BreastSubtypeR-1.4.2(bioc 3.23)

rnaseq software geneexpression classification preprocessing visualization bioconductor bioindormatics breast-cancer molecular-subtyping pam50 pam50classifier shiny

5.85 score 6 stars 13 scripts 357 downloads 16 exports 67 dependencies

Last updated from:6b2a4ab167. Checks:1 NOTE, 7 OK, 2 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	192
linux-devel	OK	948
source / vignettes	OK	279
linux-release	OK	714
macos-release	ERROR	669
macos-oldrel	ERROR	664
windows-devel	OK	1037
windows-release	OK	814
windows-oldrel	OK	1004
wasm-release	OK	151

Exports:BS_AIMS BS_cIHC BS_cIHC.itr BS_Multi BS_parker BS_PCAPAM50 BS_ssBC BS_sspbc iBreastSubtypeR InputCoverage 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 GlobalOptions glue gtable IRanges isoband iterators labeling lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig png proxy R6 RColorBrewer 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: 2026-10-31
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
Describe model-specific coverage of processed expression inputs	InputCoverage
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 1.5.12

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

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Help Manual

Usage by other packages (reverse dependencies)