What is Scanpy used for in this skill?

Scanpy is a Python-based toolkit used for analyzing single-cell gene expression data, providing tools for preprocessing, visualization, clustering, and trajectory inference.

Does it support batch correction?

Yes, the skill includes guidance for batch correction methods like ComBat to handle variation across different experimental runs.

Which data formats can I analyze?

The skill supports common single-cell formats including .h5ad (AnnData), 10X Genomics (MTX/H5), and standard CSV files.

Can I generate publication-quality plots?

Absolutely. The skill includes a dedicated plotting guide for creating high-DPI UMAPs, heatmaps, and dot plots suitable for scientific journals.

Scanpy Single-Cell Analysis

Name: Scanpy Single-Cell Analysis
Author: BbgnsurfTech

byBbgnsurfTech

•

数据科学与机器学习

Analyzes single-cell RNA-seq data using the Scanpy Python toolkit to perform quality control, clustering, and high-dimensional visualization.

This skill provides a comprehensive environment for bioinformatics and transcriptomics research, leveraging the powerful Scanpy library. It enables users to execute end-to-end single-cell workflows, from initial data ingestion of 10X and h5ad formats to advanced downstream analysis including Leiden clustering, marker gene identification, and trajectory inference. It is particularly useful for researchers who need to generate publication-quality visualizations like UMAP and t-SNE plots while maintaining best practices for data normalization and quality control.

主要功能

01Automated marker gene discovery and cluster identification

023 GitHub stars

03High-dimensional visualization via PCA, UMAP, and t-SNE

04Advanced trajectory inference and pseudotime analysis

05Support for standardized formats including .h5ad, 10X, and CSV

06Complete scRNA-seq workflow from QC to cell type annotation

使用场景

01Creating publication-ready figures and differential expression reports

02Identifying distinct cell populations and their biological markers

03Processing and filtering raw single-cell transcriptomics datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection scanpy

For use in Claude.ai and ChatGPT

Download Skill