Marker-Based Package for Single-Cell and Spatial-Transcriptomic
Annotation
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Documentation for package ‘SlimR’ version 1.0.3
Help Pages
| 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_Box | Uses "marker_list" to generate Box plot for cell annotation |
| 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_Heatmap | Uses "marker_list" to generate heatmaps 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 |
| PanglaoDB | PanglaoDB dataset |
| PanglaoDB_raw | PanglaoDB raw dataset |
| PanglaoDB_table | PanglaoDB table |
| plot_mean_expression | Counts average expression of gene set and plots Boxplot (Use in package) |
| read_excel_markers | Create "Marker_list" from Excel files ".xlsx" |
| read_seurat_markers | Create "Marker_list" from Seurat object |