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cellphonedb

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Analyze cell-cell communication with CellPhoneDB.

Data & Analytics#python#bioinformatics#ligand-receptor#single-cell#scRNA-seq#cellphonedb
AuthorKetomihine
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill enables researchers to analyze ligand-receptor-mediated cell-cell communication in single-cell datasets using CellPhoneDB, turning raw data into actionable interaction insights.

Core Features & Use Cases

  • Data preparation & validation: validates meta.txt and counts.txt formats and guides dataset setup.
  • Interaction analysis: identifies significant ligand-receptor interactions and visualizes networks.
  • Spatial & TF integration: supports microenvironment constraints and CellSign transcription factor activity integration.
  • Database management: helps manage CellPhoneDB databases, versions, and custom inputs.

Quick Start

Follow quick steps: install Python, obtain CellPhoneDB data, place your meta.txt and counts.txt in your working directory, then run METHOD 2 for significance testing and review outputs like pvalues.csv and significant_means.csv.

Dependency Matrix

Required Modules

None required

Components

references

💻 Claude Code Installation

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Please help me install this Skill:
Name: cellphonedb
Download link: https://github.com/Ketomihine/my_skills/archive/main.zip#cellphonedb

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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