anndata

SKILL.md

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