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anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

by K-Dense-AI 46k MIT Updated Sep 21, 2026
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anndata skill by K-Dense-AI
anndata — Data skill by K-Dense-AI

Overview

anndata is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabil…”. The project has 46k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/anndata`.

What anndata does

AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs), variable metadata (var), and multi-dimensional annotations (obsm, varm, obsp, varp, uns). Originally designed for single-cell genomics through Scanpy, it now serves as a general-purpose framework for any annotated data requiring efficient storage, manipulation, and analysis.

What’s inside

The SKILL.md for anndata is organised into these sections:

  • Overview
  • When to Use This Skill
  • Installation
  • Quick Start
  • Creating an AnnData object
  • Reading data
  • Writing data
  • Basic operations
  • Core Capabilities
  • 1. Data Structure
  • 2. Input/Output Operations
  • 3. Concatenation

Installation

Add anndata to your agent with:

git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/anndata

Review a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.

Supported agents

Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.

License

anndata is published under the MIT license.

Strengths

  • Clear MIT license — safe to read and adapt within its terms
  • Ships in K-Dense-AI/scientific-agent-skills, an established project with 45,887 GitHub stars
  • Actively maintained — repository updated in the last 30 days
  • Its repository gained 12,066 GitHub stars over the last 34 days

Author

K-Dense-AI 42 skills in the catalog · GitHub profile ↗
View skills

Topics

agent-skillsai-scientistbioinformaticschemoinformaticsclaudeclaude-skillsclaudecodeclinical-researchcomputational-biologydata-analysisdrug-discoverygenomicsmaterials-sciencemetabolomicsproteomicsscientific-computingscientific-visualization
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Frequently asked questions

What does anndata do?
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
How do I install anndata?
Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/anndata in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
Is anndata free to use?
Yes. anndata is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
Where does anndata come from?
anndata ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 45,887 GitHub stars apply to that whole collection, not to this skill on its own.

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