anndata

1# AnnData
2 
3## Overview
4 
5AnnData 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.
6 
7## When to Use This Skill
8 
9Use this skill when:
10- Creating, reading, or writing AnnData objects
11- Working with h5ad, zarr, or other genomics data formats
12- Performing single-cell RNA-seq analysis
13- Managing large datasets with sparse matrices or backed mode
14- Concatenating multiple datasets or experimental batches
15- Subsetting, filtering, or transforming annotated data
16- Integrating with scanpy, scvi-tools, or other scverse ecosystem tools
17 
18## Installation
19 
20Targets AnnData 0.13.4 (current PyPI release reviewed 2026-09-30), requiring Python
213.12+. Small synthetic checks cover dense/sparse matrices, native I/O, metadata,
22concatenation, and lazy reads. File paths, biological analysis, remote stores, and
23third-party integration examples are illustrative unless stated otherwise.
24 
25```bash
26uv pip install "anndata==0.13.4"
27 
28# Lazy I/O and dask-backed operations
29uv pip install "anndata[dask,lazy]==0.13.4"
30```
31 
32Use unpinned installs only when intentionally tracking the latest compatible release.
33 
34Current API notes:
35…