Changes in version 0.99.30 (2026-04-07)                 

Improvements

  - Updated both vignettes to use fully runnable toy data workflows for
    matrix, Seurat, and SingleCellExperiment inputs.
  - Removed non-justified eval = FALSE vignette chunks and aligned
    examples with the current API.
  - Updated reciprocal classification vignette examples to use reduction
    = FALSE, avoiding unsupported dimensional-reduction usage for
    recip_classif methods.
  - Standardized function and parameter naming to snake_case across the
    active package API.
  - Curated naming/style consistency in active source, including
    replacement of remaining 1:... indexing patterns.

Changes

  - Removed get.optimal_clustering from the public package
    workflow/documentation while it remains in development.

                Changes in version 0.99.21 (2024-01-27)                 

New Features

  - Initial Bioconductor submission with ground-truth-agnostic cell type
    evaluation framework
  - Support for multiple input formats: Seurat, SingleCellExperiment,
    and count matrices
  - Multiple dissimilarity methods:
      - Pseudobulk-based distances (Euclidean, Cosine, Pearson)
      - Wasserstein distance on single-cell distributions
      - Reciprocal classification approaches
  - Comprehensive internal validation metrics:
      - Silhouette scores
      - Neighborhood Purity
      - Ward's clustering consistency
      - Orbital medoid distances
      - Average similarity measures
      - 2-label silhouette analysis
  - Gene selection methods:
      - Highly variable genes (HVG) detection
      - Cell-type-specific marker identification
      - Custom gene list support
  - Dimensional reduction support (PCA, pre-computed embeddings)
  - Cross-sample and cross-study benchmarking capabilities
  - Customizable visualization tools (heatmaps, MDS, PCA plots)
  - Hierarchical clustering analysis

Improvements

  - Comprehensive documentation with vignettes
  - Examples for all 19 exported functions
  - Support for optional dependencies (transformGamPoi, glmGamPoi)
  - Efficient euclidean distance computation with custom C
    implementation
  - Parallel processing support via BiocParallel

Bug Fixes

  - Proper handling of sparse matrix formats
  - Robust batch effect handling
  - Consistent results across different label granularities

Documentation

  - Main vignette: comprehensive tutorial with real-world examples
  - Quick start guide: minimal workflow for rapid evaluation
  - Full API documentation for all exported functions