Man pages for Terkild/scutility
Utility Functions For Multi-modal Single-cell Analysis
| annotate_hierarchy | Make hierarchical named groups from SingleR annotation |
| annotate_hierarchy_MonacoImmuneData | Make hierarchical named groups from MonacoImmuneData... |
| annotate_merge_by_cluster | Merge annotation by cluster |
| annotate_SingleR | annotate individual cells with SingleR |
| barcode_rank | Calculate barcode rank |
| cell_id_hash | Generate Truncated SHA-256 Hash for Each Row of Two Columns |
| color_parentcluster | Color parent clusters by children |
| colors_get_distinct | Get a vector of more or less distinct colors |
| color_subcluster | Expand color vector for subclusters |
| cutoff_set | Helper function for calculating cutoff value |
| dimred_encircle | Encircle using KDE contours |
| dimred_encircle_add | Add encircling to ggplot |
| dimred_encircle_groups | Encircle groups using KDE contours |
| dimred_labels_add | Add labels to DimPlot (or similar ggplot2) |
| droplet_barcodes_debris | Get debris barcodes based on rank cutoff and called cell... |
| droplet_counts_per_compartment | Droplet counts per compartment |
| ggplot_set_theme | Change default ggplot theme |
| modalities_load_cellranger_count | Load Cell Ranger data and divide by modality |
| modalities_load_kallisto | Load Kallisto data by modality |
| mtx_balance | Balance/Upsample mtx |
| mtx_balance_matrix | Balance/Upsample mtx |
| mtx_load_long | Load MTX file as long format data.frame |
| mtx_long_save | Save long format mtx data.frame as mtx |
| plot_alluvial | Plot alluvial from seurat data |
| plot_barcode_rank | Barcode-Rank plot |
| plot_connected_barplot | Plot connected barplot |
| plot_dimred | Plot dimensional reduction from SCE |
| plot_dots | Plot dots |
| plot_quadrants | Plot quadrants |
| read_kallisto_data | Load and reformat kallisto output for loading |
| scVI_load | Load scVI output from adata object into SingleCellExperiment |
| seurat_annotate_SingleR | Run Annotate_SingleR on Seurat object |
| seurat_dimred_cluster_labels | Make labels for groups in DimRed plots |
| seurat_dimred_encircle_add | Encircle with Seurat meta.data |
| seurat_dimred_labels_add | Add labels to DimPlot with annotation from seurat object |
| seurat_plot_alluvial | Plot alluvial from seurat data |
| seurat_plot_connected_barplot | Plot connected barplot from seurat object |
| seurat_plot_dimred_counts | DimensionReduction with counts plot |
| subcluster_number | Number subclusters by parent cluster |
| subset_matrix | Subset a matrix |
| totalVI_load | Load totalVI output from adata object into... |
| translate_ensg_to_symbol | Translate ENSG annotation to gene symbol |
