scanpy

SKILL.md

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.

When to Use This Skill

This skill should be used when:

Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)

Performing quality control on scRNA-seq datasets

Creating UMAP, t-SNE, or PCA visualizations

Identifying cell clusters and finding marker genes

Annotating cell types based on gene expression

Conducting trajectory inference or pseudotime analysis

Generating publication-quality single-cell plots

Quick Start