NEWS

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scaper 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

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scaper 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