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anndata

Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

scientific-skills/Data Analysis/anndata/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

Use AnnData when you need to:

- Load, inspect, or export annotated single-cell datasets stored as `.h5ad` (or `zarr`) for downstream tools.
- Keep a matrix (cells × features) tightly coupled with observation/feature metadata (e.g., cell types, batches, gene annotations).
- Work efficiently with large, sparse count matrices (e.g., scRNA-seq) and avoid loading everything into memory (backed mode).
- Combine multiple experiments/batches/modalities into a unified object while tracking provenance.
- Subset/filter/transform data while preserving alignment between the matrix and metadata.

## Key Features

- **Unified container**: `X` (data matrix) plus aligned annotations: `obs`, `var`, `uns`, and multi-dimensional slots (`obsm`, `varm`, `obsp`, `varp`), plus `layers` and optional `raw`.