anndata

Topics in the source

• AnnData
• Overview
• When to Use This Skill
• Installation
• Quick Start
• Creating an AnnData object
• Reading data
• Writing data

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. 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 Understand the AnnData object structure including X, obs, var, layers, obsm, varm, obsp, varp, uns, and raw components. See: references/datastructure.md for comprehensive information on: Core components (X, obs, var, layers, obsm, varm, obsp, varp, uns, raw) Creating AnnData objects from various sources Accessing and manipulating data components Memory-efficient practices Read

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