# Machine Learning-Assisted, Marker-Based Tool for Single-Cell and Spatial Transcriptomics Annotation

## Documentation for package ‘SlimR’ version 1.0.8

- DESCRIPTION file.
- Package NEWS.

## Help Pages

calculate_cluster_variability | Calculate Cluster Variability
calculate_expression | Counts average expression of gene set (Use in package)
calculate_expression_skewness | Calculate Expression Distribution Skewness
calculate_probability | Calculate gene set expression and infer probabilities with control datasets (Use in package)
Cellmarker2 | Cellmarker2 dataset
Cellmarker2_raw | Cellmarker2 raw dataset
Cellmarker2_table | Cellmarker2 table
Celltype_Annotation | Annotate Seurat Object with SlimR Cell Type Predictions
Celltype_annotation_Cellmarker2 | Uses "marker_list" from Cellmarker2 for cell annotation
Celltype_Annotation_Combined | Uses "marker_list" to generate combined plot for cell annotation
Celltype_annotation_Excel | Uses "marker_list" from Excel input for cell annotation
Celltype_Annotation_Features | Annotate cell types using features plot with different marker databases
Celltype_Annotation_Heatmap | Uses "marker_list" to generate heatmap for cell annotation
Celltype_annotation_PanglaoDB | Uses "marker_list" from PanglaoDB for cell annotation
Celltype_annotation_Seurat | Uses "marker_list" from Seurat object for cell annotation
Celltype_Calculate | Uses "marker_list" to calculate probability, prediction results, AUC and generate heatmap for cell annotation
Celltype_Verification | Perform cell type verification and generate the validation dotplot
estimate_batch_effect | Estimate Batch Effect Strength
extract_dataset_features | Extract Dataset Characteristics for Machine Learning
generate_training_data | Generate Training Data for Machine Learning Model
Markers_filter_Cellmarker2 | Create Marker_list from the Cellmarkers2 database
Markers_filter_PanglaoDB | Create Marker_list from the PanglaoDB database
Markers_list_scIBD | List of cell type markers in the scIBD dataset
Markers_list_TCellSI | List of cell type markers in the TCellSI dataset
PanglaoDB | PanglaoDB dataset
PanglaoDB_raw | PanglaoDB raw dataset
PanglaoDB_table | PanglaoDB table
Parameter_Calculate | Adaptive Parameter Tuning for Single-Cell Data Annotation in SlimR
postprocess_parameters | Post-process Predicted Parameters
predict_optimal_parameters | Predict Optimal Parameters Using Trained Model
Read_excel_markers | Create "Marker_list" from Excel files ".xlsx"
Read_seurat_markers | Create "Marker_list" from Seurat object
train_parameter_model | Train Parameter Prediction Model