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anndata SKILL.md skillA

anndata from aicodedecode/awesome-muse-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add aicodedecode/awesome-muse-skills/anndata@git:20260927.806f3e1

Pins git:20260927.806f3e1 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: aicodedecode/awesome-muse-skills
Path: skills-imported/anndata/SKILL.md
Versions recorded: 1
Latest version: git:20260927.806f3e1, committed Sep 27, 2026
Size: 10,185 bytes
Repository stars: 25
License: MIT

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# AnnData

## Overview

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.

## When to Use This Skill

Use this skill when:
- Creating, reading, or writing AnnData objects
- Working with h5ad, zarr, or other genomics data formats
- Performing single-cell RNA-seq analysis
- Managing large datasets with sparse matrices or backed mode
- Concatenating multiple datasets or experimental batches
- Subsetting, filtering, or transforming annotated data
- Integrating with scanpy, scvi-tools, or other scverse ecosystem tools

## Installation

```bash
uv pip install anndata

# With optional dependencies
uv pip install anndata[dev,test,doc]
```

## Quick Start

### Creating an AnnData object
```python
import anndata as ad
import numpy as np
import pandas as pd

# Minimal creation
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add aicodedecode/awesome-muse-skills/anndata@sha256:70f40b01a184cfd5

The line at the top of this page pins the label git:20260927.806f3e1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_ndchoan67mnbtk47.svg)](https://markdownregistry.com/a/art_ndchoan67mnbtk47)

2 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 1 version of this file, committed on Sep 27, 2026.

version	committed	commit	size	audit
git:20260927.806f3e1 latest	2026-09-27	806f3e1	10,185 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (10185 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

aicodedecode/awesome-muse-skills · 25 stars · license MIT · pushed 2026-10-10 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_ndchoan67mnbtk47
GET https://markdownregistry.com/api/v1/resolve?ref=aicodedecode/awesome-muse-skills/anndata
GET https://markdownregistry.com/api/v1/blob/70f40b01a184cfd5cd2177c9b91bf6305ccca5f7d3a79703c698d34417712586

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.

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