NEWS

scTypeEval 0.99.30 (2026-04-07)

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.

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

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