Changes in version 1.3.1                        

Highlights (from v1.1.3 onward)

  - Paper published in NAR Genomics and Bioinformatics (2025), Editor’s
    Choice (DOI: 10.1093/nargab/lqaf131).
  - Support for raw RNA-seq counts (requires gene lengths).
  - iBreastSubtypeR refresh: cleaner UX, smarter AUTO guidance,
    consistent exports.

Enhancements

  - ssBC/ssBC.v2: singleton subgroup robustness: Subgroups with n=1 no
    longer error:
      - Keeps matrix shape (drop=FALSE) and hardens dimnames/types.
      - Primary path: original sspPredict().
        Fallback: nearest-centroid (Spearman) when needed.
      - If there are 0 common PAM50 genes, returns NA labels with shaped
        distances/dist.RORSubtype to avoid downstream errors.
      - ROR computation guarded for incomplete inputs.
  - SSPBC output now “full”: BS_sspbc() and Shiny “sspbc” runs return a
    full metrics table (not calls-only).
      - Exports map core label columns to the standard names
        (Call_5class / Call_4class when applicable).
  - Shiny: “Load example data…” button
      - One-click load of a small demo dataset from inst/RshinyTest/ to
        explore the UI without uploads.\
      - Shows a notification on success; users can immediately run
        Preprocess & map and analyses.
  - AUTO preflight UI (Shiny): Now detects cohort kind (TN, ER/HER2,
    ER-only, HER2-only) and shows compact stats:
      - ER/HER2 subgroups: ER+/HER2−, ER−/HER2−, ER+/HER2+, ER−/HER2+\
      - TN cohorts: TN vs nonTN\
      - Readiness uses the same minimums used by AUTO (sourced
        programmatically; no duplicated thresholds).
  - Shorter notifications.
    -Routine toasts (e.g., “Step 1 complete. Proceed to Step 2.”) now
    auto-dismiss sooner to reduce UI clutter.

Bug fixes

  - TN cohorts + ssBC: BS_Multi() now respects TN cohorts when methods
    are specified manually; ssBC/ssBC.v2 switch to s = "TN" / "TN.v2"
    when a TN column indicates a TN cohort. Falls back to s = "ER" /
    "ER.v2" otherwise.
  - AUTO internals: fixed variable name typo (samples_ERHER2.icd).
  - Mapping(): Robust ENTREZID coercion (from as.character() to
    as.integer() with suppressed warnings).

Shiny

  - Surface method warnings as toasts:
      - Runs are wrapped in a warning handler; package warnings (e.g.,
        ssBC.v2 singleton fallbacks) appear as yellow notifications.\
      - Warnings include subgroup, n, and example sample IDs for quick
        triage.
  - Shiny preflight reset:
      - Fixed a stale cohort summary after switching data sources
        (manual uploads ↔ example). The preflight panel now revalidates
        once inputs change.

Developer notes

  - Added lightweight internal logger ._msg() and replaced scattered
    message() calls in AUTO to standardize package output without
    affecting CRAN/Bioc checks.

Documentation

  - README/vignette: brief note on the example-data button and expected
    file locations.

Compatibility Notes

  - SSPBC “full” output keeps previous columns for calls; additional
    metrics may appear.

Upgrade Notes

  - Raw RNA-seq counts are supported from v1.1.3 onward (requires gene
    lengths).
  - If you previously parsed BS / BS.Subtype, switch to Call_5class /
    Call_4class.
  - Package API unchanged.