R: Marker-Based Package for Single-Cell and Spatial-Transcriptomic Annotation

# Marker-Based Package for Single-Cell and Spatial-Transcriptomic Annotation

## Documentation for package ‘SlimR’ version 1.0.3

- DESCRIPTION file.

## 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