Differential Analysis of Intercellular Communication from scRNA-Seq Data
Display cell-type to cell-type interactive networks
A shiny app to display scDiffCom results
Create a copy of a scDiffCom object without cci_table_raw
Filter a scDiffCom object with new filtering parameters
Return the slot distributions from a scDiffCom object
Return the slot parameters from a scDiffCom object
Return (a subset) of the slot cci_table_raw or cci_table_detected ...
Return some or all ORA tables from the slot ora_tablefrom a scDiffCo...
Display top over-represented keywords from a category of interest
Reduce scDiffCom GO Terms
Run (differential) intercellular communication analysis
Run over-representation analysis
The scDiffCom Class
Display a scDiffCom object
Analysis tools to investigate changes in intercellular communication from scRNA-seq data. Using a Seurat object as input, the package infers which cell-cell interactions are present in the dataset and how these interactions change between two conditions of interest (e.g. young vs old). It relies on an internal database of ligand-receptor interactions (available for human, mouse and rat) that have been gathered from several published studies. Detection and differential analyses rely on permutation tests. The package also contains several tools to perform over-representation analysis and visualize the results. See Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full description of the methodology.
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