CellPhoneDB Analysis

About

This skill provides a comprehensive environment for executing CellPhoneDB workflows, enabling researchers to map complex cellular communication networks from single-cell transcriptomic data. It offers deep support for data validation, statistical permutation testing, and advanced analysis methods like spatial microenvironment modeling and transcription factor integration via the CellSign module. Whether identifying significant ligand-receptor pairs, analyzing multi-subunit protein complexes, or visualizing communication pathways, this skill streamlines the entire pipeline from raw counts to biological insight.

Key Features

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• Advanced CellSign module support for linking receptors to transcription factor activity
• Management and querying of the CellPhoneDB interaction database and complex compositions
• Integration of spatial microenvironments and neighborhood-aware communication analysis
• Data validation and preprocessing for single-cell RNA-seq counts and metadata
• Statistical permutation-based testing for significant cell-type specific interactions

Use Cases

• Incorporating spatial context or transcription factor activity into cell interaction models
• Identifying ligand-receptor pairs driving communication between specific cell types in single-cell datasets
• Preparing and validating large-scale transcriptomic data for standardized communication analysis