How do I handle batch effects with this skill?

The skill supports ComBat batch correction and provides guidance on integrating with external tools like Harmony or scVI for complex datasets.

Is it suitable for creating publication-quality plots?

Yes, it includes predefined settings for high-DPI figures (300 DPI), PDF export, custom color palettes, and various plot types like dot plots and heatmaps.

Does it help with cell type annotation?

Absolutely. It provides workflows for finding marker genes via Wilcoxon rank-sum tests and mapping clusters to known cell types.

Can I use this skill for trajectory inference?

Yes, the skill includes specialized commands for PAGA (Partition-based graph abstraction) and Diffusion Pseudotime (DPT) analysis.

What data formats does the Scanpy skill support?

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

Scanpy Single-Cell Analysis

Name: Scanpy Single-Cell Analysis
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Performs comprehensive single-cell RNA-seq analysis workflows including quality control, clustering, and trajectory inference.

This skill integrates the powerful Scanpy Python toolkit into Claude's workflow, enabling automated and guided single-cell RNA-seq data analysis. It covers the entire pipeline from loading 10X or AnnData (.h5ad) files to performing advanced quality control, normalization, dimensionality reduction (UMAP/t-SNE), and Leiden clustering. It is an essential tool for bioinformaticians and researchers needing to identify marker genes, annotate cell types, or conduct trajectory and pseudotime analysis with publication-quality visualizations.

Key Features

010 GitHub stars

02End-to-end scRNA-seq pipeline from raw data to cell type annotation

03Advanced dimensionality reduction using PCA, UMAP, and t-SNE

04Automated quality control and filtering based on mitochondrial and gene counts

05Robust clustering using the Leiden algorithm with adjustable resolutions

06Publication-ready visualization tools for heatmaps, dot plots, and UMAPs

Use Cases

01Generating high-resolution figures for scientific publications and reports

02Performing trajectory inference to study cell differentiation and pseudotime

03Analyzing 10X Genomics datasets to identify distinct cell populations

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos scanpy

For use in Claude.ai and ChatGPT

Download Skill