CellCall

CellCall infers intercellular communication networks and internal regulatory signals by integrating ligand-receptor interactions, transcription factor (TF) activity, and signaling pathway activity from single-cell RNA sequencing (scRNA-seq) data.

Key Features:

• Integration of Signaling Pathways: Integrates paired ligand-receptor interactions with transcription factor (TF) activity to connect extracellular signals to intracellular regulatory responses.
• Pathway Activity Analysis: Implements an embedded pathway activity analysis method to identify significantly activated pathways mediating crosstalk between specific cell types.
• Visualizations: Generates Circos plots, Sankey plots, bubble plots, and ridge plots to visualize inferred communication networks and pathway activities.
• Case Studies: Applied to scRNA-seq datasets from human testicular cells and the tumor immune microenvironment to demonstrate inferred communications.
• Experimental Validation: Includes experimental validation supporting inferred intercellular communication and internal TF activity.
• Comparative Analyses: Performs comparative analyses with other tools to assess accuracy and functional coverage.

Scientific Applications:

• Intercellular communication mapping: Decoding intercellular signaling networks and linking extracellular ligands to intracellular TF responses using scRNA-seq data.
• Tumor microenvironment analysis: Characterizing cell-cell signaling and regulatory programs in the tumor immune microenvironment.
• Developmental biology: Investigating signaling pathways and TF-driven regulatory changes during development.
• Immunology: Analyzing immune cell communication and activation-related regulatory signals.
• Oncology: Identifying signaling interactions and transcriptional regulation relevant to tumor biology.

Methodology:

Integrates paired ligand-receptor interactions with transcription factor (TF) activity and applies an embedded pathway activity analysis to infer intercellular communication networks and intracellular regulatory signals from single-cell RNA sequencing (scRNA-seq) data.