AnnData

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.

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.

Current API notes:

• Use anndata.io for non-native read_* and write_* helpers. Top-level anndata.read_h5ad and anndata.read_zarr remain supported.
• Use ad.concat; AnnData.concatenate() was removed in 0.13. Avoid old ad.read, deprecated AnnData.*_keys() helpers and anndata.__version__; prefer explicit readers, mapping .keys(), and importlib.metadata.version("anndata").
• In 0.13, .X is also layers[None]; layer iteration includes None. Use key is not None when selecting named layers. View .X writes now use copy-on-write.
• Zarr v3 and automatic sharding are the defaults; the Python dependency is Zarr >=3. Dense H5AD X remains writable with backed="r+", but backed sparse item assignment is unsupported in 0.13.
• AnnLoader and Loom reading/writing are deprecated. AnnCollection and other experimental APIs need the caveats in the references.