Agent skill · data analytics · k-dense-ai
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.
Why this skill is useful
Provides specific commands and patterns for handling .h5ad files and integrating with the scverse ecosystem that the AI wouldn't reliably generate on its own.
What it needs
Requires python, uv installed locally. About 6k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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 Requires Python 3.11+. Current stable release: 0.12.16 (released 2026-05-18). Use unpinned installs only when intentionally tracking the latest compatible release. Current API notes: Use anndata.io for non-native read and write helpers. Top-level anndata.readh5ad and anndata.readzarr remain supported. Avoid deprecated APIs: ad.read, AnnData.concatenate(), AnnData.keys(), and anndata.version. Prefer ad.readh5ad, ad.concat, mapping .keys(), and importlib.metadata.version("anndata"). Treat anndata.experimental APIs as useful but unstable. Prefer them for large-data workflows only when their current caveats are acceptable. Quick Start Creating an AnnData object Reading data Writing data Basic operations 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/datastructure.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. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/anndata