What clustering methods are recommended within this skill?

The skill prioritizes Leiden clustering for its community-detection efficiency and biological accuracy, while also supporting Louvain and resolution-tuning.

What data formats does this Scanpy skill support?

The skill supports standard single-cell formats including 10X Genomics (.h5, .mtx), AnnData (.h5ad), and CSV files.

Can this skill help with publication-quality plots?

Yes, it includes specialized guidance for generating high-DPI, vector-format figures like UMAPs, dot plots, and heatmaps tailored for scientific journals.

Does it handle batch correction for multiple samples?

Yes, the skill provides implementation patterns for ComBat batch correction and guidance on integrating with the wider scverse ecosystem.

Scanpy Single-Cell RNA-seq Analysis

Name: Scanpy Single-Cell RNA-seq Analysis
Author: plurigrid

byplurigrid

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Data Science & ML

Performs comprehensive single-cell transcriptomics workflows including quality control, clustering, and trajectory inference using the Scanpy Python framework.

This skill equips Claude with specialized knowledge for processing and analyzing single-cell RNA-sequencing data. Built on the scalable Scanpy toolkit and AnnData structure, it provides a standardized framework for loading diverse data formats like 10X and .h5ad, performing rigorous quality control, executing dimensionality reduction via UMAP or t-SNE, and identifying cell-type-specific marker genes. It is an essential resource for bioinformaticians and researchers looking to transform raw sequencing counts into publication-quality visualizations and biological insights with AI assistance.

Key Features

01Automated quality control and filtering for mitochondrial and low-count genes

02Trajectory inference and pseudotime analysis using PAGA and DPT

03Efficient dimensionality reduction using PCA, UMAP, and t-SNE algorithms

048 GitHub stars

05Advanced clustering and cell-type annotation based on gene expression markers

06Publication-ready visualization generation for heatmaps, dot plots, and violin plots

Use Cases

01Processing 10X Genomics datasets from raw counts to annotated clusters

02Visualizing cellular development pathways through trajectory and pseudotime analysis

03Identifying differentially expressed marker genes across experimental conditions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add plurigrid/asi scanpy

For use in Claude.ai and ChatGPT

Download Skill