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anndata

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.

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# 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