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anndata — Claude Code skill: annotated matrices for single-cell data

Skill to create, read, and transform annotated data matrices in h5ad and Zarr formats. Integrates with the scverse ecosystem for transcriptomics and other metadata-rich data analysis.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -a claude-code
Open on GitHub

What anndata does

anndata stores experimental measurements (matrix X) with observation metadata, variable metadata, and multi-dimensional annotations. You can work with sparse matrices, use backed mode for large files, combine multiple datasets, and filter data by conditions.

The skill supports native h5ad and zarr formats, plus reads CSV, MTX, Loom, and 10X Genomics (via scanpy). Lazy I/O and dask operations require optional packages. Remote storage access needs internet and provider-specific fsspec adapters.

Requires Python 3.12+ and anndata 0.13.4; install via uv. Version 0.13 changes the API: use ad.concat instead of concatenate(), import readers from anndata.io, check layer names against None during iteration. Backed sparse matrices no longer support direct assignment.

What it helps with

  • read and write annotated matrices in h5ad and zarr formats
  • filter and subset data by cell or gene metadata
  • combine multiple samples or experiments into one object
  • handle large datasets in backed mode without loading into memory
  • convert between formats: CSV, MTX, Loom, 10X

Example prompts for the agent

  • Create an AnnData object from a matrix of 100 cells by 2000 genes with cell_type and sample metadata
  • Read data.h5ad in backed mode, extract the first 100 cells, and save to memory
  • Merge three datasets along observations using ad.concat, tracking the source in obs['batch']

How to install anndata

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -a claude-code

2Manually: put the files in place

~/.claude/skills/anndata/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/anndata/

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Questions about anndata

How do I install anndata in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -a claude-code. The skill will be available at ~/.claude/skills/anndata/SKILL.md.

What does anndata do?

It manages matrices where rows are cells or samples, columns are genes or measurements, and metadata is stored separately. It handles efficient storage, fast filtering, and merging of large datasets.

What Python version and dependencies are required?

Requires Python 3.12+ and anndata 0.13.4. For lazy I/O, install extras: uv pip install "anndata[dask,lazy]==0.13.4". Remote storage access needs the appropriate fsspec adapter for your provider.

See also

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