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_Annotation_PerCell
                        Annotate Seurat Object with Per-Cell SlimR
                        Predictions
Celltype_Calculate      Uses "marker_list" to calculate probability,
                        prediction results, AUC and generate heatmap
                        for cell annotation
Celltype_Calculate_PerCell
                        Per-cell annotation using marker expression and
                        optional UMAP spatial smoothing
Celltype_Compare        Compare cell type labels across two single-cell
                        datasets after aligning cell barcodes
Celltype_Verification   Perform cell type verification and generate the
                        validation dotplot
Celltype_Verification_PerCell
                        Verify per-cell annotations with marker
                        expression 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_filter_ScType   Create Marker_list from the ScType 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
ScType                  ScType dataset
ScType_raw              ScType raw dataset
ScType_table            ScType metadata table
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)
compute_adaptive_parameters
                        Compute Adaptive Parameters Based on Dataset
                        Features (Use in package)
estimate_batch_effect   Estimate Batch Effect Strength (Use in package)
extract_dataset_features
                        Extract Dataset Characteristics for Adaptive
                        Parameter Calculation (Use in package)
percell_workflow        Per-Cell Annotation Workflow Example
plot.pheatmap           Plot Method for pheatmap Objects
