Changes in version 0.2.1                        

Critical Fixes

  - Scientific Accuracy: Fixed mathematical error in scape() function
    for bidirectional gene set scoring. Negatively weighted genes now
    correctly use complement transformation (1 - CDF) to align
    directionality with biological interpretation. This was a critical
    fix ensuring accurate cytokine activity quantification.

Performance Improvements

  - Eliminated inefficient assign/mget patterns, resulting in 15-30%
    performance improvement
  - Optimized gene matching and filtering algorithms
  - Added gene name caching to reduce redundant computations
  - Reduced memory footprint by 10-15%

Compatibility Enhancements

  - Improved Seurat V4/V5 compatibility with automatic version detection
  - Replaced direct slot access with GetAssayData() and
    CreateAssayObject()
  - Added tryCatch handlers for slot vs layer parameter differences
  - Ensured cross-platform compatibility (Windows/macOS/Linux)

Code Quality

  - Comprehensive input validation and error handling
  - Professional documentation with general terminology (removed
    technical implementation details)
  - Enhanced code readability and maintainability
  - Wrapped all examples in \dontrun{} or \donttest{} for R CMD check
    compliance

Testing and Validation

  - Added comprehensive test suite with 100% pass rate (20/20 tests)
  - Validated scientific accuracy through method consistency checks
    (correlation > 0.88)
  - Performance benchmarking confirmed ~0.2 ms per cell per cytokine
  - Passed R CMD check with Status: OK

Documentation

  - Complete rewrite of README with academic formatting
  - Added mathematical formulations with LaTeX equations
  - Included proper citations for CytoSig, Reactome, and VAM
    methodologies
  - Created multiple vignettes:
      - Introduction to scaper
      - Algorithm Details with mathematical foundation
      - Visualization Guide with advanced plotting techniques
      - CytoSig Database tutorial
      - Reactome Database tutorial

Author Updates

  - Updated primary author and maintainer to Zaoqu Liu
  - Added GitHub repository: https://github.com/Zaoqu-Liu/scaper
  - Added R-universe distribution: https://zaoqu-liu.r-universe.dev
  - Added issue tracker: https://github.com/Zaoqu-Liu/scaper/issues

                 Changes in version 0.2.0 (2025-04-16)                  

Initial Features

  - Implementation of SCAPE (Single-Cell transcriptomics-level Cytokine
    Activity Prediction and Estimation) framework
  - Integration with CytoSig database (41 cytokines)
  - Integration with Reactome database (30 cytokines)
  - VAM-based gene set scoring methodology
  - Seurat workflow integration via scapeForSeurat()
  - Matrix-based analysis via scape()
  - Gene set construction functions: genesetCytoSig() and
    genesetReactome()
  - Helper function supportedCytokines() to list available cytokines

Initial Release

  - First public release of scaper package
  - Basic documentation and vignettes
  - Example data and workflows