AnnData

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

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)