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 Requires Python 3.11+. Current stable release: 0.12.16 (released 2026-05-18). ```bash uv pip install "anndata==0.12.16" # Lazy I/O and dask-backed operations uv pip install "anndata[dask,lazy]==0.12.16" # Development / docs (contributors) uv pip install "anndata[dev,test,doc]==0.12.16" ``` 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. - Avoid deprecated APIs: `ad.read`, `AnnData.concatenate...