Is the anndata skill free?

Yes. The skill itself is free from K-Dense-AI/scientific-agent-skills. SkillProof publishes the install command and an independent test verdict at no cost.

What is the anndata SkillProof Score?

7.6/10 — installs cleanly 5/5, triggers reliably 4/5, output vs. baseline 5/10, docs & honesty 5/5.

How do I install anndata?

Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.

Can I use anndata with Cursor, Copilot, Gemini CLI, Codex or other AI tools?

The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.

anndata

Works with .h5ad annotated matrix files for single-cell data in the scverse ecosystem.

by K-Dense-AI · K-Dense-AI/scientific-agent-skills

Works with setup

Install — copy the command Download source ↗

Test report

Verdict: Works with setup
Score: 7.6/10
Tested: Jul 11, 2026
Environment: Claude Code 2.x (agent harness)
Upstream re-checked: Aug 10, 2026 · fb8a68e

Verbatim install (git clone + cp) works cleanly; SKILL.md frontmatter parses as strict YAML with all 5 referenced files present, and every documented API (AnnData construction, ad.concat, sparse conversion, h5ad backed-mode I/O, zarr settings) runs correctly against the real anndata package. On an A/B build-and-filter-an-AnnData task the skill and base arms produced functionally identical, correct, idiomatic scripts (both dropped the all-zero cell, both wrote/reloaded h5ad in backed mode) so the skill added no measurable output advantage on this task. Requires the anndata Python package installed (pip install anndata); no API keys or external services needed.

Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works

Installs cleanly 5/5
Triggers reliably 4/5
Output vs. baseline 5/10
Docs & honesty 5/5

What anndata does

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 to install anndata

git clone https://github.com/K-Dense-AI/scientific-agent-skills
cd scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r skills/anndata ~/.claude/skills/anndata

Skills live in ~/.claude/skills/ (global) or .claude/skills/ (per-project). Restart Claude Code after installing.

Commands — how to trigger anndata

/anndata Works with .h5ad annotated matrix files for single-cell data in the scverse ecosystem.

It also activates on plain-language prompts like these:

Load and inspect this .h5ad single-cell dataset
Convert my single-cell data into an AnnData object
Subset this AnnData file by cell type

Frequently asked questions

Is the anndata skill free?: Yes. The skill itself is free from K-Dense-AI/scientific-agent-skills. SkillProof publishes the install command and an independent test verdict at no cost.
Does anndata work with Claude Code?: We tested it with Claude Code 2.x (agent harness) on Jul 11, 2026. Verdict: Works with setup. Verbatim install (git clone + cp) works cleanly; SKILL.md frontmatter parses as strict YAML with all 5 referenced files present, and every documented API (AnnData construction, ad.concat, sparse conversion, h5ad backed-mode I/O, zarr settings) runs correctly against the real anndata package. On an A/B build-and-filter-an-AnnData task the skill and base arms produced functionally identical, correct, idiomatic scripts (both dropped the all-zero cell, both wrote/reloaded h5ad in backed mode) so the skill added no measurable output advantage on this task. Requires the anndata Python package installed (pip install anndata); no API keys or external services needed.
What is the anndata SkillProof Score?: 7.6/10 — installs cleanly 5/5, triggers reliably 4/5, output vs. baseline 5/10, docs & honesty 5/5.
How do I install anndata?: Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
Can I use anndata with Cursor, Copilot, Gemini CLI, Codex or other AI tools?: The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.