Changelog

Source: NEWS.md

Connectome 1.0.2

New Features

• Added comprehensive vignettes:
  • Introduction to Connectome
  • Algorithm Principles and Mathematical Framework
  • Visualization Gallery
  • Differential Connectivity Analysis
  • Best Practices and Troubleshooting
• Built pkgdown documentation site

Improvements

• Improved cross-platform compatibility using Seurat::GetAssayData() instead of direct slot access
• Replaced deprecated Seurat::SubsetData() with modern subset() approach
• Replaced library() calls with requireNamespace() checks for better CRAN compliance
• Fixed Inf value handling in differential analysis plots using is.infinite()
• Updated ggplot2::element_rect() from deprecated size to linewidth
• Replaced 1:length() patterns with safer seq_along() for boundary condition handling
• Improved performance by replacing rbind() in loops with pre-allocation

Bug Fixes

• Fixed scientific accuracy issue in DOR calculation by applying Haldane-Anscombe correction (pseudocount = 0.5)
• Fixed PercentExpression function to use Seurat::Assays() instead of internal function

Documentation

• Updated author information (Zaoqu Liu as maintainer)
• Added GitHub repository URLs
• Cleaned up function documentation

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Connectome 1.0.1

• Initial release based on original Connectome package
• Multi-species ligand-receptor database support (human, mouse, rat, pig)
• Network construction and visualization functions
• Differential connectivity analysis