API for patrickCNMartin/Vesalius
Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data
| Global functions | |
|---|---|
| add_active_count_tag | Man page Source code |
| add_active_embedding_tag | Man page Source code |
| add_cells | Source code |
| add_counts | Man page Source code |
| add_embeddings | Man page Source code |
| add_integration_tag | Source code |
| adjust_cooridnates | Source code |
| adjust_counts | Man page Source code |
| align_index | Man page Source code |
| as.Seurat.vesalius_assay | Source code |
| as.SingleCellExperiment.vesalius_assay | Source code |
| as.SpatialExperiment.vesalius_assay | Source code |
| as.anndata.vesalius_assay | Source code |
| assign_centers | Man page Source code |
| average_embed | Man page Source code |
| back_infer | Man page Source code |
| bubble_stack | Man page |
| build_mapped_assay | Man page Source code |
| build_vesalius_assay | Man page Source code |
| calculate_scale | Man page |
| cell_type_match | Man page Source code |
| check_barcodes | Man page Source code |
| check_binary_nature | Man page Source code |
| check_cell_labels | Source code |
| check_cells | Man page Source code |
| check_coordinates | Man page Source code |
| check_cost_contribution | Source code |
| check_cost_matrix_validity | Source code |
| check_cost_validity | Source code |
| check_counts | Man page Source code |
| check_deg_method | Man page Source code |
| check_dim_selection_method | Man page Source code |
| check_embed_methods | Man page Source code |
| check_embedding_selection | Man page Source code |
| check_embeddings | Man page Source code |
| check_eq_method | Man page Source code |
| check_feature_integration | Source code |
| check_features | Man page Source code Source code |
| check_for_unmatched | Source code |
| check_for_zero_counts | Man page Source code |
| check_gene_overlap | Source code |
| check_genes | Source code |
| check_group_value | Man page Source code |
| check_image | Man page Source code |
| check_image_input | Man page Source code |
| check_inputs | Man page Source code |
| check_isolation_method | Man page Source code |
| check_map_input | Source code |
| check_map_selection | Source code |
| check_maps | Source code |
| check_metric_trial | Source code |
| check_min_spatial_index | Man page Source code |
| check_norm | Man page Source code |
| check_norm_methods | Man page Source code |
| check_sample | Source code |
| check_segment_trial | Man page Source code |
| check_segmentation_method | Man page Source code |
| check_signal | Source code |
| check_smoothing_kernel | Man page Source code |
| check_smoothing_level | Man page Source code |
| check_template_source | Source code |
| check_tensor_compression | Man page Source code |
| check_territory_trial | Man page Source code |
| check_tiles | Man page Source code |
| chunk | Source code |
| clean_trial | Source code |
| coef_of_var | Source code |
| commit_log | Man page Source code |
| compute_effect_size | Man page Source code |
| compute_nearest_neighbor_graph | Man page Source code |
| concat_cost | Man page Source code |
| concat_embed | Man page Source code |
| concat_matches | Man page Source code |
| connected_pixels | Source code |
| convexify | Man page Source code |
| coordinates | Man page |
| counts | Man page |
| create_alpha | Man page Source code |
| create_commit_log | Man page Source code |
| create_palette | Man page Source code |
| create_pseudo_centroids | Man page Source code |
| create_trial_tag | Man page Source code |
| detect_edges | Man page Source code |
| dispatch_batch | Man page Source code |
| dispatch_cost_groups | Man page Source code |
| dispatch_deg_group | Man page Source code |
| dispatch_sample | Man page Source code |
| dispatch_territory | Man page Source code |
| dispersion | Source code |
| distance_pooling | Man page Source code |
| ecdf_eq | Man page Source code |
| embed_latent_space | Man page Source code |
| embed_lsi | Man page Source code |
| embed_lsi_umap | Man page Source code |
| embed_nmf | Man page Source code |
| embed_pca | Man page Source code |
| embed_pcal | Man page Source code |
| embed_umap | Man page Source code |
| equalize_image | Man page Source code |
| extend_boundary | Man page Source code |
| filter_assay | Source code |
| filter_cost | Source code |
| filter_grid | Man page Source code |
| filter_maps | Man page Source code |
| filter_tiles | Man page Source code |
| format_c_to_ves | Man page Source code |
| format_call | Man page Source code |
| format_counts_for_deseq2 | Man page Source code |
| format_counts_for_edger | Man page Source code |
| format_counts_for_logit | Man page Source code |
| format_ves_to_c | Man page Source code |
| future_ves_to_cimg | Man page Source code |
| generate_embeddings | Man page Source code |
| generate_spix | Man page Source code |
| generate_tiles | Man page Source code |
| get_active_count_tag | Man page Source code |
| get_active_embedding_tag | Man page Source code |
| get_assay_names | Man page Source code |
| get_coordinates | Man page Source code |
| get_cost | Source code |
| get_cost_contribution | Man page Source code |
| get_counts | Man page Source code |
| get_deg_metrics | Man page Source code |
| get_embeddings | Man page Source code |
| get_func_from_commit | Man page Source code |
| get_mapping_scores | Source code |
| get_markers | Man page Source code |
| get_metric_clusters | Man page Source code |
| get_neighborhood_signal | Man page Source code |
| get_range | Source code |
| get_signal | Man page Source code |
| get_territories | Man page Source code |
| get_tiles | Man page Source code |
| gini | Source code |
| globalise_territories | Man page Source code |
| graph_from_voronoi | Source code |
| graph_neighborhood | Man page Source code |
| graph_path_length | Man page |
| hclust_scores | Man page Source code |
| identify_markers | Man page Source code |
| image_plot | Man page Source code |
| initialize_matches | Man page Source code |
| int_sctransform | Man page Source code |
| integrate_assays | Man page Source code |
| integrate_counts | Man page Source code |
| interlace_embeds | Man page Source code |
| internal_smooth | Man page Source code |
| isolate_territories | Man page Source code |
| jaccard_cost | Source code |
| jitter_coord | Man page |
| jitter_counts | Man page |
| joint_territories | Man page Source code |
| kmeans_segmentation | Man page Source code |
| knn_neighborhood | Man page Source code |
| layer_territory | Man page Source code |
| leiden_scores | Man page Source code |
| leiden_segmentation | Man page Source code |
| leiden_slic_segmentation | Source code |
| listify | Source code |
| log_norm | Man page Source code |
| louvain_scores | Man page Source code |
| louvain_segmentation | Man page Source code |
| louvain_slic_segmentation | Source code |
| make_composition_matrix | Source code |
| map_assays | Man page Source code |
| map_index | Man page Source code |
| match_cells | Man page Source code |
| merge_coordinates | Man page Source code |
| merge_territories | Man page Source code |
| message_switch | Man page Source code |
| min_max | Man page Source code |
| neighborhood_signal | Man page Source code |
| niche_composition | Man page Source code |
| no_norm | Man page Source code |
| norm_pixel | Man page Source code |
| optimize_matching | Man page Source code |
| order_labels | Source code |
| overlap_distance_matrix | Man page Source code |
| pearson_approx | Man page Source code |
| pearson_exact | Source code |
| pearson_fast | Source code |
| poc | Source code |
| point_mapping | Man page Source code |
| populate_graph | Man page Source code |
| process_counts | Man page Source code |
| radius_neighborhood | Man page Source code |
| rasterise | Man page Source code |
| rebalence_colors | Man page Source code |
| reduce_tensor_resolution | Man page Source code |
| regularise | Man page Source code |
| regularise_image | Man page Source code |
| rename_counts | Man page Source code |
| score_matches | Man page Source code |
| search_log | Man page Source code |
| segment_image | Man page Source code |
| select_initial_indices | Man page |
| select_similar | Source code |
| signal_similarity | Man page Source code |
| simple_bar | Source code |
| slic_segmentation | Source code |
| smooth_image | Man page Source code |
| som_segmentation | Source code |
| summarise_territories | Man page Source code |
| territory_convex | Source code |
| territory_edge | Source code |
| territory_morphing | Man page Source code |
| territory_neighborhood | Man page Source code |
| territory_plot | Man page Source code |
| tfidf_norm | Man page Source code |
| unpack_territory_path | Man page Source code |
| update_matches | Man page Source code |
| update_vesalius_assay | Man page Source code |
| vesalius | Man page |
| vesalius-package | Man page |
| vesalius_assay-class | Man page |
| vesalius_deg | Man page Source code |
| vesalius_deg_chisq | Man page Source code |
| vesalius_deg_deseq2 | Man page Source code |
| vesalius_deg_edger | Man page Source code |
| vesalius_deg_fisher | Man page Source code |
| vesalius_deg_logit | Man page Source code |
| vesalius_deg_ttest | Man page Source code |
| vesalius_deg_wilcox | Man page Source code |
| vesalius_package | Man page |
| view_gene_expression | Man page Source code |
| view_mapping_metrics | Source code |
