SlimR 1.0.8 (2025-10-08)
- This version adds the function of machine learning (e.g., ‘Random
Forest’, ‘Gradient Boosting’, ‘Support Vector Machine’, ‘Ensemble
Learning’) for cell types calculate parameter recognition.
- Optimize the data filter mode of “Markers_list_scIBD” in the
package, and filter through
sort_by = "logFC"
and
gene_filter = 20
parameter.
- Adjust the calculation process of the ‘FSS’ value in the
read_seurat_markers()
function when ‘resources’ is set to
‘presto’.
- Optimize the prompt output during the execution of the
Celltype_Verification()
function.
- Modify and optimize README and NEWS file.
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.