# Anndata

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and...

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Engineering
- License: BSD-3-Clause license
- Last updated: 2026-10-26
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill anndata -g -a gemini-cli -y`

## Description

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

Targets AnnData 0.13.4 (current PyPI release reviewed 2026-09-30), requiring Python
3.12+. Small synthetic checks cover dense/sparse matrices, native I/O, metadata,
concatenation, and lazy reads. File paths, biological analysis, remote stores, and
third-party integration examples are illustrative unless stated otherwise.

```bash
uv pip install "anndata==0.13.4"

# Lazy I/O and dask-backed operations
uv pip install "anndata[dask,lazy]==0.13.4"
```

Use unpinned installs only when intentionally tracking the latest compatible release.

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/anndata/SKILL.md