anndata

Name: anndata
Author: K-Dense-AI

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.

anndata

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---
name: anndata
description: 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.
license: BSD-3-Clause license
metadata:
    skill-author: K-Dense Inc.
---

# AnnData

## Overview

AnnData is a Python package for handling annotated data matrices, storin

How to Use

Recommended: Install to project (local)

mkdir -p .claude/skills
curl -o .claude/skills/anndata.md \
  https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/main/scientific-skills/anndata/SKILL.md

Skill is scoped to this project only. Add .claude/skills/ to your .gitignoreif you don't want to commit it.

Alternative: Clone full repo

git clone https://github.com/K-Dense-AI/claude-scientific-skills

Then reference at scientific-skills/anndata/SKILL.md

Related Skills

scanpy

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.

data-aiscanpy

by sickn33 (Antigravity) · antigravity-awesome-skills

scanpy

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

scanpyscanpy

by K-Dense-AI · claude-scientific-skills