anndata

name	anndata
description	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.

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

uv pip install anndata

# With optional dependencies
uv pip install anndata[dev,test,doc]

Quick Start

Creating an AnnData object

import anndata as ad
import numpy as np
import pandas as pd

# Minimal creation
X = np.random.rand(, )  
adata = ad.AnnData(X)


obs = pd.DataFrame({
    : [, ] * ,
    : [, ] * 
}, index=[  i  ()])

var = pd.DataFrame({
    : [  i  ()]
}, index=[  i  ()])

adata = ad.AnnData(X=X, obs=obs, var=var)