Scanpy

If you're analyzing single-cell RNA-seq data, this gives Claude the full scanpy toolkit for the standard workflow: loading h5ad or 10X files, running QC on cell and gene counts, normalizing with log transforms, computing PCA and UMAP embeddings, running Leiden clustering at different resolutions, and identifying marker genes with Wilcoxon tests. The skill includes practical defaults like filtering cells with over 5% mitochondrial counts and using 2000 highly variable genes. It's built around the AnnData object structure, so Claude understands how to access expression matrices, metadata, and embeddings. Really solid for going from raw counts to annotated cell types without writing the boilerplate yourself.

skills.sh installs: 325
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill scanpy --agent claude-code

Installs into .claude/skills of the current project.

Files

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

Basic Import and Setup

import scanpy as sc
import pandas as pd
import numpy as np

# Configure settings
# sc.settings.verbosity = 'hint'  # enable for debugging
sc.settings.figdir = './figures/'
sc.print_header()  # in notebooks

Loading Data

# From 10X Genomics
adata = sc.read_10x_mtx('path/to/data/')
adata = sc.read_10x_h5('path/to/data.h5')

SKILL.md on GitHub

Details

Repository: github.com/davila7/claude-code-templates
First seen: Jun 3, 2026