NEWS.md

In SlimR: Marker-Based Package for Single-Cell and Spatial-Transcriptomic Annotation

SlimR 1.0.7 (2025-08-19)

• Added new function Celltype_Verification() for predicted cell types validation and generate the validation dotplot.
• Optimize the function 'Read_seurat_markers()'. This is compatible with the 'presto::wilcoxauc()' source tag, and the 'Feature Significance Score' (FSS, product value of log2FC and Expression ratio) can be calculated and sorted accordingly.
• Add custom color parameters colour_low and colour_high to all ploting output functions.
• Renamed Celltype_annotation_Dotplot() to Celltype_Annotation_Features(), Celltype_annotation_Box() to Celltype_Annotation_Combined(), read_seurat_markers() to Read_seurat_markers(), read_excel_markers() to Read_excel_markers() for unified function naming structure.
• Enhanced README with detailed process descriptions.
• Optimized message output system for cleaner console feedback.
• Resolved various code bugs reported by users.
• Modified codebase to meet CRAN standards and policies.

SlimR 1.0.6 (2025-08-06)

• Integrated "scIBD" human intestine reference database.
• Added AUC calculation and visualization to Celltype_Calculate().
• Implemented AUC-based prediction correction in cell typing.
• Streamlined code output formatting.
• Fixed critical bugs in prediction pipeline.
• Modified code to meet CRAN submission requirements.

SlimR 1.0.5 (2025-08-05)

• Added "TCellSI" T-cell reference database.
• Introduced Celltype_Calculate() for automated scoring.
• Added Celltype_Annotation() for end-to-end cell typing.
• Improved message output system.
• Resolved multiple code errors.
• Modified code to meet CRAN standards and policies.

SlimR 1.0.4 (2025-07-30)

• Optimized Celltype_annotation_Heatmap() performance.
• Enhanced probability calculation in calculate_probability().
• Modified code to meet CRAN submission requirements.
• Change the License type from "GPL-3" to "MIT".

SlimR 1.0.3 (2025-07-28)

• Replaced calculate_mean_expression() with calculate_probability() in Celltype_annotation_Heatmap().
• Modified code to meet CRAN standards and policies.

SlimR 1.0.1 (2025-07-19)

• Changed Celltype_annotation_Bar() to Celltype_annotation_Box() with improved visualization capabilities.

SlimR 1.0.0 (2025-07-07)

• Initial release of SlimR package with core cell type annotation framework and basic visualization functions.

SlimR documentation built on Aug. 19, 2025, 1:13 a.m.