anndata
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
npx skills add LeonChaoX/qinyan-academic-skills --skill anndata --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 ```bash uv pip install anndata # With optional dependencies uv pip install anndata[dev,test,doc] ``` ## Quick Start ### Creating an AnnData object ```python 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
- Overview
- When to Use This Skill
- Installation
- Quick Start
- Creating an AnnData object
- Reading data
- Writing data
- Basic operations
- Core Capabilities
- 1. Data Structure
- 2. Input/Output Operations
- 3. Concatenation
- 4. Data Manipulation
- 5. Best Practices
uv pip install anndata With optional dependencies uv pip install anndata[dev,test,doc]
What does the anndata skill do?
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill anndata --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.