Changes in version 1.1.1                        

Bug Fixes and Maintenance

This patch release addresses minor issues identified after the
initial 1.0.0 release while preserving all core functionality. Key fixes
include:

  - Resolved input validation edge cases in the subtyping pipeline
  - Enhanced handling of cohorts with extreme ER+ ratios in AUTO mode
  - Corrected data type handling for raw counts input
  - Updated documentation typos and parameter descriptions

All core features remain fully functional:

  - Comprehensive Intrinsic Subtyping for Breast Cancer: Integrates
    multiple published intrinsic subtyping methods, including NC-based
    approaches like the original PAM50 (Parker et al., J Clin
    Oncol, 2009) and SSP-based methods like AIMS (Paquet et al., J Natl
    Cancer Inst, 2015).
  - Multi-Method Subtyping Functionality: Simultaneously predicts breast
    cancer intrinsic subtypes using a variety of validated methods for
    comparative analysis.
  - AUTO Mode Feature: Evaluates the distribution of ER and HER2 status
    in the test cohort to automatically select subtyping methods that
    align with the cohort's characteristics, ensuring compatibility with
    method-specific assumptions for greater accuracy and reliability.
  - Optimized Gene Mapping: Optimizes gene mapping using Entrez IDs to
    maximize the inclusion of genes across subtyping methods.
  - Streamlined Input and Output: Provides standardized input/output
    formats to ensure smooth integration with other gene expression
    analysis tools.
  - User-Friendly Shiny App Interface: Features a web-based GUI that
    runs entirely locally, ensuring data privacy with no online sharing,
    ideal for users who prefer a visual interface over R scripting.

Users can safely upgrade from v1.0.0 for improved stability.