anndata

combined

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools. 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.

When to use

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
Load, inspect, or export annotated single-cell datasets stored as `.h5ad` (or `zarr`) for downstream tools.

Skill page

Conflict

The K-Dense copy is the most current and technically precise, containing specific 0.13.4 API changes (e.g., `anndata.io` module, removal of `AnnData.concatenate`, Zarr v3 defaults) that the other two lack. However, the aipoch and FreedomIntelligence copies provide a more complete 'runnable' example workflow (including `ad.concat` and `strings_to_categoricals`) and a clearer 'When to Use' section that the K-Dense copy truncates or omits in its quick start. Because the K-Dense copy is the only one with the critical version-specific API constraints, but the others have better pedagogical examples, crowning one would hide either the version safety or the workflow completeness.