cellchat-cell-communication

Name: cellchat-cell-communication
Availability: InStock
Author: jaechang-hits

Infer and visualize intercellular communication networks from single-cell RNA-seq data using CellChat.

298|27|Updated Feb 18, 2026

Search Tags:#bioinformatics #network analysis #single-cell #cell communication #rna-seq #cellchat

Ready to run

npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill cellchat-cell-communication

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cellchat-cell-communication
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/cellchat-cell-communication
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill cellchat-cell-communication

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires CellChat, Seurat, NMF, ggplot2, ggalluvial, igraph, dplyr, patchwork, reticulate, circlize, RColorBrewer, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the inference, analysis, and visualization of intercellular communication networks from single-cell RNA-seq data, revealing how different cell types interact within a tissue or biological system.

Core Features & Use Cases

Infer Interactions: Identify ligand-receptor pairs mediating communication between cell groups.
Pathway Analysis: Aggregate interactions into signaling pathways (e.g., VEGF, MHC-II).
Network Visualization: Generate chord diagrams, heatmaps, and bubble plots to explore communication patterns.
Use Case: Understand how tumor cells communicate with immune cells in the tumor microenvironment to identify potential therapeutic targets.

Quick Start

Use the cellchat-cell-communication skill to infer and visualize cell-cell communication pathways from your Seurat object.

Frequently Asked Questions about cellchat-cell-communication

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I infer cell-cell communication networks from single-cell RNA-seq data?▼

You can infer cell-cell communication networks from single-cell RNA-seq data by identifying ligand-receptor interactions between cell groups using the CellChat R package, which aggregates interactions into signaling pathways.

Can I visualize single-cell signaling pathways using chord diagrams and heatmaps?▼

Yes, you can visualize single-cell signaling pathways using chord diagrams, heatmaps, and bubble plots to explore communication patterns and quantify cell group roles as senders, receivers, or influencers.

Does CellChat work with Seurat objects for cell communication analysis?▼

Yes, CellChat works with Seurat objects for cell communication analysis, allowing you to directly infer and visualize intercellular communication pathways from your prepared single-cell RNA-seq data.

What is cell-cell communication analysis in the tumor microenvironment?▼

Cell-cell communication analysis in the tumor microenvironment identifies how tumor cells communicate with immune cells via ligand-receptor pairs, revealing signaling pathways to help identify potential therapeutic targets.

Does CellChat support both human and mouse single-cell RNA-seq data?▼

Yes, CellChat supports both human and mouse single-cell RNA-seq data, allowing you to map intercellular communication networks and analyze signaling pathways across these two model organisms.

What is the best way to identify ligand-receptor interactions mediating communication between cell groups?▼

The best way to identify ligand-receptor interactions mediating communication between cell groups is using CellChat, which quantifies cell group roles and aggregates interactions into signaling pathways for comprehensive network analysis.