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(100, 2000)  # 100 cells × 2000 genes
adata = ad.AnnData(X)

# With metadata
obs = pd.DataFrame({
    'cell_type': ['T cell', 'B cell'] * 50,
    'sample': ['A', 'B'] * 50
}, index=[f'cell_{i}' for i in range(100)])

var = pd.DataFrame({
    'gene_name': [f'Gene_{i}' for i in range(2000)]
}, index=[f'ENSG{i:05d}' for i in range(2000)])

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

Reading data

# Read h5ad file
adata = ad.read_h5ad('data.h5ad')

# Read with backed mode (for large files)
adata = ad.read_h5ad('large_data.h5ad', backed='r')

# Read other formats
adata = ad.read_csv('data.csv')
adata = ad.read_loom('data.loom')
adata = ad.read_10x_h5('filtered_feature_bc_matrix.h5')

Writing data

# Write h5ad file
adata.write_h5ad('output.h5ad')

# Write with compression
adata.write_h5ad('output.h5ad', compression='gzip')

# Write other formats
adata.write_zarr('output.zarr')
adata.write_csvs('output_dir/')

Basic operations

# Subset by conditions
t_cells = adata[adata.obs['cell_type'] == 'T cell']

# Subset by indices
subset = adata[0:50, 0:100]

# Add metadata
adata.obs['quality_score'] = np.random.rand(adata.n_obs)
adata.var['highly_variable'] = np.random.rand(adata.n_vars) > 0.8

# Access dimensions
print(f"{adata.n_obs} observations × {adata.n_vars} variables")

Core Capabilities

1. Data Structure

Understand the AnnData object structure including X, obs, var, layers, obsm, varm, obsp, varp, uns, and raw components.

See: references/data_structure.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

2. Input/Output Operations

Read and write data in various formats with support for compression, backed mode, and cloud storage.

See: references/io_operations.md for details on:

• Native formats (h5ad, zarr)
• Alternative formats (CSV, MTX, Loom, 10X, Excel)
• Backed mode for large datasets
• Remote data access
• Format conversion
• Performance optimization

Common commands:

# Read/write h5ad
adata = ad.read_h5ad('data.h5ad', backed='r')
adata.write_h5ad('output.h5ad', compression='gzip')

# Read 10X data
adata = ad.read_10x_h5('filtered_feature_bc_matrix.h5')

# Read MTX format
adata = ad.read_mtx('matrix.mtx').T

3. Concatenation

Combine multiple AnnData objects along observations or variables with flexible join strategies.

See: references/concatenation.md for comprehensive coverage of:

• Basic concatenation (axis=0 for observations, axis=1 for variables)
• Join types (inner, outer)
• Merge strategies (same, unique, first, only)
• Tracking data sources with labels
• Lazy concatenation (AnnCollection)
• On-disk concatenation for large datasets

Common commands:

# Concatenate observations (combine samples)
adata = ad.concat(
    [adata1, adata2, adata3],
    axis=0,
    join='inner',
    label='batch',
    keys=['batch1', 'batch2', 'batch3']
)

# Concatenate variables (combine modalities)
adata = ad.concat([adata_rna, adata_protein], axis=1)

# Lazy concatenation
from anndata.experimental import AnnCollection
collection = AnnCollection(
    ['data1.h5ad', 'data2.h5ad'],
    join_obs='outer',
    label='dataset'
)

4. Data Manipulation

Transform, subset, filter, and reorganize data efficiently.

See: references/manipulation.md for detailed guidance on:

• Subsetting (by indices, names, boolean masks, metadata conditions)
• Transposition
• Copying (full copies vs views)
• Renaming (observations, variables, categories)
• Type conversions (strings to categoricals, sparse/dense)
• Adding/removing data components
• Reordering
• Quality control filtering

Common commands:

# Subset by metadata
filtered = adata[adata.obs['quality_score'] > 0.8]
hv_genes = adata[:, adata.var['highly_variable']]

# Transpose
adata_T = adata.T

# Copy vs view
view = adata[0:100, :]  # View (lightweight reference)
copy = adata[0:100, :].copy()  # Independent copy

# Convert strings to categoricals
adata.strings_to_categoricals()

5. Best Practices

Follow recommended patterns for memory efficiency, performance, and reproducibility.

See: references/best_practices.md for guidelines on:

• Memory management (sparse matrices, categoricals, backed mode)
• Views vs copies
• Data storage optimization
• Performance optimization
• Working with raw data
• Metadata management
• Reproducibility
• Error handling
• Integration with other tools
• Common pitfalls and solutions

Key recommendations:

# Use sparse matrices for sparse data
from scipy.sparse import csr_matrix
adata.X = csr_matrix
how to use anndata
CursorClaude CodeClineCodexWindsurfGooseGitHub CopilotVS CodeGemini CLIKiloOpencodeKimi CLIRoo ClineAiderContinueZedBolt.newLovablev0Replit AgentSweepSmol DeveloperDevinCavemanAmpAntigravity
How to use anndata on Cursor
AI-first code editor with Composer
1
Prerequisites
Before installing skills in Cursor, ensure your development environment meets these requirements:
›Cursor installed and configured on your development machine
›Node.js version 16.0+ with npm package manager (verify with node --version)
›Active project directory or workspace where you want to add anndata
2
Execute installation command
Execute the skills CLI command in your project's root directory to begin installation:
$npx skills add https://github.com/davila7/claude-code-templates --skill anndatacopy
The skills CLI fetches anndata from GitHub repository davila7/claude-code-templates and configures it for Cursor.
3
Select Cursor when prompted
The CLI will show a list of available agents. Use arrow keys to navigate and space to select Cursor:
◆ Which agents do you want to install to?
│
│ ── Universal (.agents/skills) ── always included ────
│   • Amp
│   • Antigravity
│   • Cline
│   • Codex
│ ●Cursor(selected)
│   • Cursor
│   • Windsurf
4
Verify installation
Confirm successful installation by checking the skill directory location:
.cursor/skills/anndata
Reload or restart Cursor to activate anndata. Access the skill through slash commands (e.g., /anndata) or your agent's skill management interface.
⚠
Security & Verification Notice
We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.
Skills execute code in your development environment. Always verify the publisher's identity, review recent commits, and test in isolated environments before production deployment.
Additional Resources
›View source code on GitHub›Skills CLI documentation›Learn more about Cursor›What are agent skills?