AnnData (Claude Skill)

Claude skill that documents the AnnData object model — X, obs, var, layers, obsm, varm, obsp, varp, uns, and raw — and the read/write/subset/concatenate operations used in single-cell pipelines.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — actively maintained 2025–2026
Pricing Free / OSS
Capabilities Read/Write — Claude executes AnnData via Python/Bash

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/single-cell/anndata-data-structure into ~/.claude/skills/).
  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the anndata skill when prompted (also works in Cursor/Codex via the Agent Skills spec; requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone of the source repo: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/anndata ~/.claude/skills/
pip install anndata

What it does

SKILL.md with recipes for:

  • AnnData object structure (X, obs, var, layers, obsm/varm, obsp/varp, uns, raw)
  • Reading and writing .h5ad, .zarr, and 10x formats, including compression and backed mode
  • Combining objects along observations or variables with flexible join strategies
  • Subsetting, filtering, layer manipulation, and reorganization for downstream Scanpy / scvi-tools workflows

Primary use cases: Standardising single-cell input formats, joining multiple datasets, debugging Scanpy / scvi-tools pipelines that consume AnnData.

Notes

AnnData itself is a Python library, not a Claude-installable component. This entry catalogs the K-Dense skill wrapper; the underlying library must still be pip installed in the environment Claude executes in.

Sources

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