Cellmarker2             Cellmarker2 dataset
Cellmarker2_raw         Cellmarker2 raw dataset
Cellmarker2_table       Cellmarker2 table
Celltype_Annotation     Annotate Seurat Object with SlimR Cell Type
                        Predictions
Celltype_Annotation_Combined
                        Uses "marker_list" to generate combined plot
                        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_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
Celltype_annotation_Cellmarker2
                        Uses "marker_list" from Cellmarker2 for cell
                        annotation
Celltype_annotation_Excel
                        Uses "marker_list" from Excel input 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
Markers_filter_Cellmarker2
                        Create Marker_list from the Cellmarkers2
                        database
Markers_filter_PanglaoDB
                        Create Marker_list from the PanglaoDB database
Markers_list_PCTAM      List of Macrophage subtype markers in the
                        article "Macrophage diversity in cancer
                        revisited in the era of single-cell omics"
Markers_list_PCTIT      List of T cell subtype markers in the article
                        "Pan-cancer single cell landscape of
                        tumor-infiltrating T cells"
Markers_list_TCellSI    List of T cell subtype markers in the article
                        TCellSI
Markers_list_scIBD      List of cell type markers in the article scIBD
PanglaoDB               PanglaoDB dataset
PanglaoDB_raw           PanglaoDB raw dataset
PanglaoDB_table         PanglaoDB table
Parameter_Calculate     Adaptive Parameter Tuning for Single-Cell Data
                        Annotation in SlimR
Read_excel_markers      Create "Marker_list" from Excel files ".xlsx"
Read_seurat_markers     Create "Marker_list" from Seurat object
calculate_cluster_variability
                        Calculate Cluster Variability (Use in package)
calculate_expression    Counts average expression of gene set (Use in
                        package)
calculate_expression_skewness
                        Calculate Expression Distribution Skewness (Use
                        in package)
calculate_probability   Calculate gene set expression and infer
                        probabilities with control datasets (Use in
                        package)
estimate_batch_effect   Estimate Batch Effect Strength (Use in package)
extract_dataset_features
                        Extract Dataset Characteristics for Machine
                        Learning (Use in package)
generate_training_data
                        Generate Training Data for Machine Learning
                        Model (Use in package)
postprocess_parameters
                        Post-process Predicted Parameters (Use in
                        package)
predict_optimal_parameters
                        Predict Optimal Parameters Using Trained Model
                        (Use in package)
train_parameter_model   Train Parameter Prediction Model (Use in
                        package)
