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Anndata

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davila7·vlatest·data·MIT

This skill facilitates efficient data handling for AnnData objects, a crucial format in single-cell analysis, streamlining workflows and improving performance.

Repository

Install on your platform

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 davila7/claude-code-templates --skill anndata -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

Publisher

davila7

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Install target

Live repository

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About this skill

The anndata skill enables AI agents to load, inspect, and manipulate AnnData objects, a standard format for storing single-cell genomics data containing both observations (cells) and variables (genes). It allows agents to perform subsetting, filtering, and basic statistical operations directly within the Python environment.

When to use it

  • Loading .h5ad or .h5 files created by tools like Scanpy or Seurat for immediate analysis.
  • Inspecting metadata structures such as obs, var, and uns dictionaries before processing biological data.
  • Subsetting datasets to isolate specific cell populations or gene clusters based on defined criteria.
  • Converting raw AnnData objects into Pandas DataFrames for visualization or custom statistical modeling.

Key capabilities

  • File Loading: Reads standard AnnData file formats (.h5ad, .h5) efficiently.
  • Structure Inspection: Accesses and displays obs (observations), var (variables), and uns (unstructured data) attributes.
  • Data Manipulation: Supports subsetting rows and columns to filter cells or genes dynamically.
  • Format Conversion: Transforms AnnData objects into Pandas DataFrames for broader compatibility.

Example prompts

  • "Load the file 'my_data.h5ad' and display the first 10 rows of the observation metadata."
  • "Filter this AnnData object to keep only cells where the 'cell_type' is 'T_cell' and show the resulting shape."
  • "Convert the current AnnData object into a Pandas DataFrame containing only the gene expression matrix."

Tips & gotchas

Ensure your AI agent has access to the anndata Python package installed in its environment, as file paths must be absolute or relative to the working directory. Large single-cell datasets may require significant memory; verify hardware constraints before loading massive .h5ad files.