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Single Cell Cellphonedb Communication Mapping

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starlitnightly·vlatest·productivity·GPL-3.0

This skill maps cellular communication networks using Cellphonedb data, streamlining research and understanding complex biological interactions.

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Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add omicverse/omicverse --skill single-cell-cellphonedb-communication-mapping -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

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starlitnightly

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Live repository

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About this skill

What it does

This skill allows AI agents to communicate with and map data from CellphoneDB, a database for single-cell genomics data. It facilitates querying the database using specific parameters and retrieving relevant information about cell populations, gene expression, and other cellular characteristics. The agent can then use this retrieved data for analysis or visualization purposes.

When to use it

  • Identifying cell types: Ask the AI to find all cells expressing a particular marker gene within a CellphoneDB dataset.
  • Comparing datasets: Query two different CellphoneDB databases and identify differences in cell population proportions.
  • Analyzing gene expression patterns: Retrieve average gene expression values for specific cell populations from a CellphoneDB database.
  • Generating visualizations: Request the AI to generate plots or tables summarizing data extracted from CellphoneDB, such as UMAP embeddings colored by cell type.

Key capabilities

  • Querying CellphoneDB databases
  • Retrieving cell population information
  • Accessing gene expression data
  • Data mapping and visualization support

Example prompts

  • "Find all cells in dataset 'my_dataset' that express the marker gene 'CD45'."
  • "Compare the proportion of T cells between datasets 'dataset1' and 'dataset2'."
  • "What is the average expression level of gene 'MYC' in cell type 'B cells' from database 'public_db'?"

Tips & gotchas

  • Requires familiarity with CellphoneDB data structure and terminology.
  • The agent’s performance depends on the accuracy and completeness of the underlying CellphoneDB dataset.