Differential Analysis of Intercellular Communication from
scRNA-Seq Data
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Documentation for package ‘scDiffCom’ version 1.0.0
Help Pages
| BuildNetwork | Display cell-type to cell-type interactive networks |
| BuildNetwork-method | Display cell-type to cell-type interactive networks |
| BuildShiny | A shiny app to display scDiffCom results |
| BuildShiny-method | A shiny app to display scDiffCom results |
| EraseRawCCI | Create a copy of a scDiffCom object without 'cci_table_raw' |
| EraseRawCCI-method | Create a copy of a scDiffCom object without 'cci_table_raw' |
| FilterCCI | Filter a scDiffCom object with new filtering parameters |
| FilterCCI-method | Filter a scDiffCom object with new filtering parameters |
| gene_ontology_level | All gene ontology terms annotated with their levels |
| GetDistributions | Return the slot 'distributions' from a scDiffCom object |
| GetDistributions-method | Return the slot 'distributions' from a scDiffCom object |
| GetParameters | Return the slot 'parameters' from a scDiffCom object |
| GetParameters-method | Return the slot 'parameters' from a scDiffCom object |
| GetTableCCI | Return (a subset) of the slot 'cci_table_raw' or 'cci_table_detected' from a scDiffCom object |
| GetTableCCI-method | Return (a subset) of the slot 'cci_table_raw' or 'cci_table_detected' from a scDiffCom object |
| GetTableORA | Return some or all ORA tables from the slot 'ora_table' from a scDiffCom object |
| GetTableORA-method | Return some or all ORA tables from the slot 'ora_table' from a scDiffCom object |
| LRI_human | A collection of human ligand-receptor interactions. |
| LRI_mouse | A collection of mouse ligand-receptor interactions. |
| LRI_rat | A collection of rat ligand-receptor interactions. |
| PlotORA | Display top over-represented keywords from a category of interest |
| PlotORA-method | Display top over-represented keywords from a category of interest |
| ReduceGO | Reduce scDiffCom GO Terms |
| ReduceGO-method | Reduce scDiffCom GO Terms |
| RunORA | Run over-representation analysis |
| RunORA-method | Run over-representation analysis |
| run_interaction_analysis | Run (differential) intercellular communication analysis |
| scDiffCom-class | The scDiffCom Class |
| seurat_sample_tms_liver | A down-sampled Seurat object to use for testing and benchmarking |
| show-method | Display a scDiffCom object |