API for scDiffCom
Differential Analysis of Intercellular Communication from scRNA-Seq Data
| Global functions | |
|---|---|
| BuildNetwork | Man page |
| BuildNetwork,scDiffCom-method | Man page |
| BuildShiny | Man page |
| BuildShiny,scDiffCom-method | Man page |
| EraseRawCCI | Man page |
| EraseRawCCI,scDiffCom-method | Man page |
| FilterCCI | Man page |
| FilterCCI,scDiffCom-method | Man page |
| GetDistributions | Man page |
| GetDistributions,scDiffCom-method | Man page |
| GetParameters | Man page |
| GetParameters,scDiffComBase-method | Man page |
| GetTableCCI | Man page |
| GetTableCCI,scDiffCom-method | Man page |
| GetTableORA | Man page |
| GetTableORA,scDiffCom-method | Man page |
| LRI_human | Man page |
| LRI_mouse | Man page |
| LRI_rat | Man page |
| PlotORA | Man page |
| PlotORA,scDiffCom-method | Man page |
| ReduceGO | Man page |
| ReduceGO,scDiffCom-method | Man page |
| RunORA | Man page |
| RunORA,scDiffCom-method | Man page |
| add_cell_number | Source code |
| add_edge_color | Source code |
| add_edge_layout | Source code |
| add_sample_number | Source code |
| add_vertex_layout | Source code |
| aggregate_cells | Source code |
| apply_visnetwork | Source code |
| build_LRI | Source code |
| build_cci_or_drate | Source code |
| build_edge_table | Source code |
| build_igraph | Source code |
| build_interactive_network | Source code |
| build_ora_dt | Source code |
| build_vertex_table | Source code |
| build_visnetwork | Source code |
| clean_colnames | Source code |
| clip_infinite_OR | Source code |
| combine_LR_db | Source code |
| create_LR_CellPhoneDB | Source code |
| create_cci_template | Source code |
| edge_annotation_html | Source code |
| edges_legend | Source code |
| extract_LRI_inputs | Source code |
| extract_additional_category_counts | Source code |
| extract_analysis_inputs | Source code |
| extract_category_counts | Source code |
| extract_condition_inputs | Source code |
| extract_edge_metadata | Source code |
| extract_seurat_inputs | Source code |
| extract_vertex_metadata | Source code |
| filter_celltypes | Source code |
| fisher_2sided | Source code |
| gene_ontology_level | Man page |
| get_ECM_genes | Source code |
| get_GO_LEVELS | Source code |
| get_GO_interactions | Source code |
| get_KEGG_PWS_interactions | Source code |
| get_network_components | Source code |
| get_orthologs | Source code |
| get_table_cci | Source code |
| get_tables_ora | Source code |
| get_visnetwork_interactive | Source code |
| get_visnetwork_options | Source code |
| imbalance_ratio | Source code |
| interactive_from_igraph | Source code |
| kulc | Source code |
| merge_LR_orthologs | Source code |
| nodes_legend | Source code |
| perform_ora_from_counts | Source code |
| plot_ora | Source code |
| prepare_LR_CellChat | Source code |
| prepare_LR_CellPhoneDB | Source code |
| prepare_LR_CellTalkDB | Source code |
| prepare_LR_ICELLNET | Source code |
| prepare_LR_NicheNet | Source code |
| prepare_LR_SingleCellSignalR | Source code |
| prepare_LR_connectomeDB2020 | Source code |
| process_cci_raw | Source code |
| process_celltype_ER_enrichment | Source code |
| process_celltype_pairs_enrichment | Source code |
| reduce_go_terms | Source code |
| rescale_internal | Source code |
| run_filtering_and_ora | Source code |
| run_interaction_analysis | Man page Source code |
| run_internal_raw_analysis | Source code |
| run_ora | Source code |
| run_simple_cci_analysis | Source code |
| run_stat_analysis | Source code |
| run_stat_iteration | Source code |
| scDiffCom-class | Man page |
| setup_graph_config | Source code |
| setup_layout | Source code |
| seurat_sample_tms_liver | Man page |
| show,scDiffCom-method | Man page |
| sort_bipartite_vertices | Source code |
| validate_parameters | Source code |
| validate_reduced_go_table | Source code |
| validate_slot_cci_table_detected | Source code |
| validate_slot_cci_table_raw | Source code |
| validate_slot_distributions | Source code |
| validate_slot_is_combined | Source code |
| validate_slot_ora_stringent | Source code |
| validate_slot_ora_table | Source code |
| validate_slot_parameters | Source code |
| vertex_annotation_html | Source code |
| vfisher_2sided | Source code |
