Scanpy: Single-Cell Analysis

Overview

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.

In the bundled Vibe-Skills routing surface, this skill also absorbs the former AnnData and scVI/scANVI route surfaces. Use it for h5ad container handling and scverse latent-model planning when those tasks appear inside a single-cell workflow.

When to Use This Skill