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Create Cellchat Obj Specifications

Process Details

  • Name: create_cellchat_obj
  • Process UUID: e0c21e94da7a404899868f8948d93130
  • Process Group: cellchat2

Overview

This process creates a CellChat object from single-cell RNA sequencing data for cell-cell communication analysis. CellChat is a computational framework that infers and analyzes intercellular communication networks from single-cell transcriptomic data by identifying ligand-receptor interactions and signaling pathways between different cell types.

This process is implemented in Bash, which invokes an R script for CellChat object creation and communication network inference.

Key Functionality

  • CellChat Object Creation: Converts Seurat objects into CellChat format for communication analysis
  • Database Integration: Incorporates organism-specific ligand-receptor interaction databases
  • Cell Communication Inference: Identifies potential cell-cell communication pathways based on gene expression
  • Data Preprocessing: Applies smoothing, trimming, and filtering based on minimum cell requirements
  • Report Generation: Creates R Markdown documentation for downstream signaling analysis

Input/Output Specification

Inputs

Required Inputs

  • RDS File
    • Description: Seurat object containing single-cell RNA-seq data with cell type annotations
    • Format: RDS file

Outputs

  • RDS File

    • Description: CellChat object containing processed communication data and inferred signaling networks
    • Format: RDS

  • R Markdown

    • Description: Template R Markdown file for signaling analysis and visualization
    • Format: RMD

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Cell Identity Column

    • Description: Column name in metadata specifying cell type identities
    • Default value: Configured via ident parameter

  • Organism

    • Description: Species for ligand-receptor database selection
    • Default value: Configured via organism parameter

  • Database Type

    • Description: Type of interaction database to use for communication inference
    • Default value: Configured via db_type parameter

  • Smoothing

    • Description: Whether to apply data smoothing for communication inference
    • Default value: Configured via smooth parameter

  • Cell Groups

    • Description: Specific cell groups to include in the analysis
    • Default value: Configured via cell_groups parameter

  • Source Cells

    • Description: Specific source cell types for communication analysis
    • Default value: FALSE (all cell types)

  • Target Cells

    • Description: Specific target cell types for communication analysis
    • Default value: FALSE (all cell types)

  • Trim Parameter

    • Description: Trimming threshold for data preprocessing
    • Default value: Configured via trim parameter

  • Minimum Cells

    • Description: Minimum number of cells required per cell type for inclusion
    • Default value: Configured via min_cells parameter

References & Resources

  • Tool Documentation: Contact the team for details on create_cellchat_obj.R
  • Related Papers: Jin, S., Guerrero-Juarez, C.F., Zhang, L. et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 12, 1088 (2021). https://doi.org/10.1038/s41467-021-21246-9