What is BreastSubtypeR?

BreastSubtypeR is an R/Bioconductor package for intrinsic molecular subtyping of breast cancer. It brings widely used predictors—PAM50 variants (e.g., ssBC/ssBC.v2), AIMS, and others—into one reproducible workflow with harmonized inputs/outputs and clear defaults, enabling consistent reporting across datasets in research and translational studies.

Why it matters

Subtype calls often differ across methods and cohorts, complicating comparisons and meta-analyses. BreastSubtypeR provides reproducible preprocessing/mapping, side-by-side method outputs, and a consistent export schema—so teams can assess agreement and run cross-cohort analyses with greater consistency and transparency.
Important: BreastSubtypeR is for research/translational use; Prosigna® is the clinical PAM50 assay.

What’s new in v1.2.0

• Raw RNA-seq counts support (requires gene lengths)

• iBreastSubtypeR refresh: cleaner UX, smarter AUTO guidance, consistent exports

• Quality & fixes: TN-cohort handling for ssBC/ssBC.v2; clarified AUTO internals; refined, data-informed thresholds

Key features

• AUTO mode selects sensible subtyping strategies per dataset (guided by cohort composition and data characteristics), reducing method-driven variation in research analyses.

• RNA-seq support: accepts raw counts (gene lengths needed) and pre-normalized inputs, with clear mapping/normalization guidance.

• Shiny GUI (iBreastSubtypeR): point-and-click exploration (with bundled example data).

• Rich outputs: method results side-by-side; exports map labels to Call_5class / Call_4class where applicable.

Get started (Bioconductor release)

Paper (peer-reviewed)

NAR Genomics & Bioinformatics — Editor’s Choice: https://doi.org/10.1093/nargab/lqaf131

Links

• Bioconductor (release): https://www.bioconductor.org/packages/release/bioc/html/BreastSubtypeR.html

• GitHub (latest): https://github.com/yqkiuo/BreastSubtypeR

Who should use this

• Clinical researchers exploring subtype-guided hypotheses or retrospective/translational cohorts

• Biologists linking subtype calls to pathways/TME phenotypes

• Bioinformaticians running reproducible, multi-cohort RNA-seq analyses

Acknowledgments

Qiao Yang; Johan Hartman; colleagues at Karolinska Institutet; the Bioconductor community.

Disclaimer

For research/translational use only; Prosigna® is the clinical PAM50 assay.