Man pages for gillislab/MetaMarkers
Extract robust markers from multiple datasets
| assign_cells | Assign cells to a cell type based on maximum marker scores. |
| compute_aurocs | Efficient computation of AUROCs (vectorized for predictors... |
| compute_marker_enrichment | Compute marker enrichment (score over expected score, under... |
| compute_markers | Compute differential expression statistics for given dataset... |
| compute_umap | Compute UMAP coordinates for a target dataset. |
| convert_to_cpm | Convert expression matrix to CPM (library size... |
| design_matrix | Convert character vector to one-hot encoded matrix, with one... |
| export_markers | Export marker statistics to file. |
| export_markers_by_cell_type | Export marker statistics to file, one file per cell type. |
| export_markers_by_group | Export markers statistics to file, one file per group. |
| export_markers_for_cell_type | Export marker statistics of given cell type to file. |
| export_meta_markers | Export meta-analytic markers to file (including header with... |
| export_meta_markers_by_cell_type | Export meta-analytic markers to file (one file per cell... |
| get_cell_type | Extract cell type information from a cell type label. |
| get_group | Extract group information from a cell type label. |
| get_pareto_markers | Get Pareto front markers (best markers) of given cell type in... |
| make_meta_markers | Extract meta-analytic markers from multiple datasets. |
| marker_list_to_matrix | Convert marker list to gene x cell type matrix |
| marker_table_to_matrix | Convert marker table to gene x cell type matrix |
| plot_assignments | Plot cell type assignments in UMAP space. |
| plot_marker_expression | Plot expression of markers in cell type as violin plots. |
| plot_marker_scores | Plot markers scores in UMAP space (one facet per marker set). |
| plot_pareto_markers | Plot best markers in the (fold change of detection, AUROC)... |
| plot_pareto_summary | Plot Pareto fronts (best markers) of all cell types in the... |
| read_markers | Import marker statistics. |
| read_meta_markers | Import meta-marker statistics. |
| remove_duplicated_genes | Remove duplicate gene from a marker table (individual... |
| score_cells | Compute marker scores (average marker expression) in a target... |
| summarize_auroc | Compute separability (AUROC) of cell types based on marker... |
| summarize_fold_change | Compute signal-to-noise ratio (fold change) of cell types... |
| summarize_precision_recall | Compute annotation performance of cell types based on marker... |
