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Function reference

Intercellular communication analysis

run_interaction_analysis()
Run (differential) intercellular communication analysis

scDiffCom S4 class

scDiffCom-class
The scDiffCom Class

Visualization

BuildShiny()
A shiny app to display scDiffCom results
BuildNetwork()
Display cell-type to cell-type interactive networks
PlotORA()
Display top over-represented keywords from a category of interest
show(<scDiffCom>)
Display a scDiffCom object

Accessors

GetParameters()
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
GetTableORA()
Return some or all ORA tables from the slot ora_table from a scDiffCom object
GetDistributions()
Return the slot distributions from a scDiffCom object

Utilities

ReduceGO()
Reduce scDiffCom GO Terms
RunORA()
Run over-representation analysis
FilterCCI()
Filter a scDiffCom object with new filtering parameters
EraseRawCCI()
Create a copy of a scDiffCom object without cci_table_raw

Data

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.
gene_ontology_level
All gene ontology terms annotated with their levels
seurat_sample_tms_liver
A down-sampled Seurat object to use for testing and benchmarking