Published September 16, 2025 | Version 1.1.3
Software Open

BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research

Authors/Creators

  • 1. ROR icon Karolinska Institutet
  • 2. Karolinska University Hospital

Contributors

Project leader:

Project member:

Research group:

  • 1. ROR icon Karolinska Institutet
  • 2. ROR icon Karolinska University Hospital

Description

Introduction

BreastSubtypeR is an R/Bioconductor package for intrinsic molecular subtyping of breast cancer in research settings. It unifies multiple established classifiers and introduces an assumption-aware AUTO mode that inspects cohort characteristics and routes data to cohort-appropriate methods. A local Shiny GUI (iBreastSubtypeR) is included for exploratory use and QC.

Key features

  • Unified interface to multiple subtyping methods (PAM50, AIMS, ssBC, sspbc, cIHC, etc.)

  • AUTO mode: cohort-aware method selection with guardrails

  • Reproducible preprocessing and QC outputs

  • Shiny app for interactive review (iBreastSubtypeR)

Installation

Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("BreastSubtypeR")

GitHub

# install.packages("remotes")
remotes::install_github("JohanHartmanGroupBioteam/BreastSubtypeR")

Quick start

library(BreastSubtypeR)
 
# Example data
data("BreastSubtypeRobj")
data("OSLO2EMIT0obj")
 
data_input <- Mapping(OSLO2EMIT0obj$se_obj, RawCounts = FALSE)
res_auto <- BS_Multi(data_input = data_input, methods = "AUTO")
 
# Launch Shiny:
BreastSubtypeR::iBreastSubtypeR()

Scope

Research use only; in clinical practice, intrinsic molecular subtyping is standardized via approved diagnostics (e.g., Prosigna®).

Provenance

Built from commit 9112d81e8538f3debb6c101255008486d052c326 of the GitHub repository:
https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR
(The exact commit is also listed under Related identifiers.)

How to cite

  • Software: Use this Zenodo record’s DOI.
  • Article: Yang Q, Hartman J, Sifakis EG. BreastSubtypeR: Intrinsic molecular subtyping toolkit for breast cancer research. NAR Genomics & Bioinformatics. 2025; https://doi.org/10.1093/nargab/lqaf131

Files

Files (6.8 MB)

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Additional details

Related works

Is derived from
Software: https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR/commit/9112d81e8538f3debb6c101255008486d052c326 (URL)
Is documented by
Conference paper: 10.5281/zenodo.17080602 (DOI)
Is supplement to
Journal article: 10.1093/nargab/lqaf131 (DOI)
Software: https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR (URL)
Software: 10.18129/B9.bioc.BreastSubtypeR (DOI)

Dates

Created
2025-09-12

Software

Repository URL
https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR/
Programming language
R
Development Status
Active

References

  • Yang Q, Hartman J, Sifakis EG, BreastSubtypeR: Intrinsic molecular subtyping toolkit for breast cancer research. NAR Genomics & Bioinformatics. 2025; doi:10.1093/nargab/lqaf131