# Differential Analysis of Intercellular Communication from scRNA-Seq Data

## Documentation for package ‘scDiffCom’ version 1.0.0

- DESCRIPTION file.
- Package NEWS.

## 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