Changes in version 1.1.8 Highlights - 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. - Refined, data-driven thresholds for ER/HER2 skew detection in AUTO. - Broader input-validation across the subtyping pipeline. Bug Fixes - AUTO: fixed ER/HER2 strata messaging for ER+/HER2− and ER−/HER2− cohorts. The spurious message “ssBC.v2 for samples: ERnegHER2neg” no longer appears in ER+/HER2− cohorts. - AUTO: in pure HER2+ cohorts, ssBC.v2 is now preferred as intended; ssBC is not listed or subset-indexed there. - AUTO: ssBC / ssBC.v2 sample-subsetting and messages now occur only when that method is actually selected. - PAM50 variants no longer error with calibration = "None" or "External". - ssBC variants handle datasets with <50 PAM50 genes more robustly. - Fixed data.frame issue (“check.names matched by multiple arguments”) via safe builders. - Removed duplicate “Subtype == BS_*class” columns in downloads. - Safer ROR merges on PatientID with clearer notifications. - Eliminated jsonlite named-vector warning in plotting. Changes - Documentation: clarified guidance for subtype-specific cohorts: - ER/HER2-defined cohorts (ER+/HER2−, ER−/HER2−, ER+/HER2+, ER−/HER2+): NC-based → ssBC.v2 only; plus SSP-based (AIMS, sspbc). - ER-only (ER+ or ER−) and TNBC: NC-based → ssBC and/or ssBC.v2 (subject to minimum sizes); plus SSP-based. - AUTO clarifications (simulation-based defaults): - ER balance gate: lower_ratio = 0.39, upper_ratio = 0.69. - Minimum sizes: ER+ total = 15, ER− total = 18, TN total = 18. - Subgroup gates (rounded): ER+ subgroups (HER2+ / HER2−) use round(15 / 2); ER− subgroups (HER2+ / HER2−) use round(18 / 2). - Notes: these thresholds gate method eligibility; they do not force a consensus call. Details in the vignette (“AUTO logic”). Shiny (iBreastSubtypeR) - New hero card + method chips (NC, SSP, ROR, AUTO) and “Why AUTO?” explainer modal. - AIMS: 4-class toggle disabled (AIMS is 5-class only). - AUTO/AIMS/SSPBC: Full-metrics export selector hidden. - Clear per-method help + PAM50 calibration notes. - Small UX polish: file dialogs + Mapping preserve scroll position. Exports - Two modes: Calls only and Full metrics (incl. ROR when available). - Standard column names: Call_5class / Call_4class (internal BS / BS.Subtype mapped). - AUTO: Calls = selected-k table (+ entropy); Full = selected-k merged with other-k (suffix _4class / _5class). - Filenames encode method, class, and mode (e.g., results-PAM50-5class-full.txt). Behavior & Validation - ROR only for NC methods when TSIZE/NODE exist and are numeric (auto coercion + warnings). - Stricter checks for ssBC subgroups (ER/HER2/TN presence and coding). - AUTO preflight warns on missing or mis-coded ER/HER2. Core Features (unchanged) - Unified NC (PAM50, cIHC, PCAPAM50, ssBC) and SSP (AIMS, SSPBC) subtyping under one API. - BS_Multi with cohort-aware AUTO selection; Mapping for platform-agnostic preprocessing. - Interactive Shiny app with Bioconductor-friendly exports. 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.