Integrated the ScType marker database for tissue-aware cell type
annotation.
Added Markers_filter_ScType() for filtering ScType
markers by tissue type and cell name.
Added ScType, ScType_raw, and
ScType_table data objects.
Version 1.1.1 (2026-02-05)
This release introduces a major new feature for fine-grained cell
type identification alongside significant improvements to accuracy,
performance, and usability.
New Feature: Per-Cell Annotation System
Added a new workflow for annotating individual cells, complementing
the existing cluster-based approach.
Offers three scoring methods: weighted (default),
mean, and AUCell.
Includes optional UMAP-based spatial smoothing to improve annotation
consistency.
Major Improvements to Per-Cell Annotation
Introduced an adaptive min_score = "auto" threshold
that scales with the number of cell types, preventing excessive
“Unassigned” labels in large marker sets (e.g., 30+ types).
Added a new min_confidence parameter for ratio-based
filtering, providing more robust cell type discrimination than simple
score differences.
Enhanced the weighted scoring method with new marker
specificity and IDF-like weights.
Improved the AUCell method with adaptive
n_top calculation and a combined binary/rank-weighted
scoring strategy.
Annotation results now include a Raw_score_matrix and a
Parameters list for better reproducibility and
debugging.
Performance & Stability
Optimized for large datasets with vectorized operations and
memory-efficient processing.
Integrated the RANN package for optional 10-100x faster
k-NN computations in spatial smoothing.
Added comprehensive validation and error handling in core functions
like compute_adaptive_parameters().
Testing & Documentation
Added a comprehensive test suite with 147 tests covering core
functionality, NA handling, and workflows.
Reorganized documentation and README with clearer distinctions
between cluster-based and per-cell annotation.
Version 1.1.0 (2026-01-20)
Improvements
Optimized AUC calculation in Celltype_Calculate() to
use individual gene AUCs for more robust predictions.
Enhanced the adaptive machine learning algorithm in
Parameter_Calculate() for better model generalization.
Extended Parameter_Calculate() to include threshold
parameter prediction.
Updated general documentation and README structure.
Version 1.0.9 (2025-12-18)
New Features
Integrated two new pan-cancer immune cell reference databases:
PCTIT: Pan-cancer T cell markers.
PCTAM: Pan-cancer macrophage markers.
Improvements
Added a has_colnames parameter to
Read_excel_markers() to support reading Excel files without
column headers.
Updated documentation.
Version 1.0.8 (2025-10-08)
New Features
Implemented machine learning-based parameter recognition using
Random Forest, Gradient Boosting, SVM, and an Ensemble learner.
Improvements
Optimized data filtering for the Markers_list_scIBD
database.
Enhanced FSS (Fraction of Samples Significant) calculation in
Read_seurat_markers() for outputs from the
presto package.
Improved console output formatting in
Celltype_Verification().
Version 1.0.7 (2025-08-19)
New Features
Added the Celltype_Verification() function for
generating validation dot plots.
Introduced custom color parameters (colour_low,
colour_high) for all plotting functions.
Improvements
Enhanced Read_seurat_markers() with better
compatibility for FindMarkers results from the
presto package.
Standardized function names across the package for consistency.
Improved the internal messaging system for clearer user
feedback.
General updates for CRAN compliance.
Bug Fixes
Resolved various user-reported issues.
Version 1.0.6 (2025-08-06)
New Features
Integrated the scIBD human intestine cell reference database.
Added AUC (Area Under the Curve) calculation and visualization to
the Celltype_Calculate() function.
Implemented AUC-based prediction correction.
Improvements
Streamlined the formatting of function outputs.
General updates for CRAN compliance.
Bug Fixes
Fixed critical bugs in the core prediction pipeline.
Version 1.0.5 (2025-08-05)
New Features
Added the TCellSI T-cell reference database.
Introduced the Celltype_Calculate() function for
automated cluster scoring.
Introduced the Celltype_Annotation() function for an
end-to-end annotation workflow.
Improvements
Enhanced the console message output system.
General updates for CRAN compliance.
Bug Fixes
Resolved multiple code errors.
Version 1.0.4 (2025-07-30)
Improvements
Optimized the performance of the
Celltype_annotation_Heatmap() function.
Enhanced the probability calculation in the helper function
calculate_probability().
Changed the package license from GPL-3 to MIT.
General updates for CRAN compliance.
Version 1.0.3 (2025-07-28)
Improvements
Updated Celltype_annotation_Heatmap() to use the new
calculate_probability() function.
General updates for CRAN compliance.
Version 1.0.1 (2025-07-19)
Changes
Renamed Celltype_annotation_Bar() to
Celltype_annotation_Box() and improved its visualization
output.
Version 1.0.0 (2025-07-07)
Initial release on CRAN.
Provides the core framework for cluster-based cell type annotation
and visualization.
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