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Changelog

Source: NEWS.md

fastCNV 2.0.0

Major Improvements

Performance Optimization

  • Vectorized CNV classification algorithm (O(n) complexity)
  • Optimized sliding window computation with efficient matrix operations
  • Improved memory management with strategic garbage collection

Code Quality

  • Consistent use of TRUE/FALSE instead of T/F
  • Replaced 1:length() with seq_along() for safer iteration
  • Fixed column reference in regionToForce parameter handling

Compatibility

  • Full compatibility with Seurat 4.x and 5.x
  • Robust CreateAssayObject handling across SeuratObject versions
  • Fixed list subsetting ([[]] vs []) for proper object access

Documentation

  • Academic-style README with methodology description
  • Comprehensive vignettes with algorithm explanations
  • R-universe integration for easy installation

Bug Fixes

  • Fixed regionToForce using incorrect column name (chromosome_name → chromosome_num)
  • Fixed potential dimension mismatch in CNVCallingList
  • Fixed color mapping in plotCNVResultsHD for ComplexHeatmap

fastCNV 1.5.0

Bug Fixes

  • Fixed subscript out of bounds in CNVCalling
  • Fixed subscript out of bounds in CNVCallingList
  • Fixed .GetSeuratCompat() error
  • Fixed CreateAssayObject compatibility

Compatibility

  • Works with Seurat 4.4.0 + SeuratObject 4.1.4
  • Replaced SCTransform with standard workflow
  • Added comprehensive error handling

fastCNV 1.0.0

Initial Release

  • CNV inference from scRNA-seq and spatial transcriptomics data
  • Sliding window-based algorithm
  • Reference cell normalization
  • Hierarchical clustering of CNV profiles
  • Phylogenetic tree construction
  • Heatmap and tree visualization

Credits

Original fastCNV developed by Gadea Cabrejas and Clarice Groeneveld. Enhanced and maintained by Zaoqu Liu.