Can I use this for trajectory inference?

Yes, the skill provides specific workflows for PAGA (Partition-based graph abstraction) and diffusion pseudotime analysis.

Is the visualization customizable for publications?

Absolutely. The skill includes a dedicated plotting guide and high-resolution settings for generating frame-free PDF plots suitable for scientific journals.

How does it handle batch effects?

It includes guidance for ComBat batch correction and provides references for integrating with other tools like Harmony or scVI.

What file formats does this Scanpy skill support?

The skill 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: x-cmd

byx-cmd

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データサイエンスとML

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

Scanpy is a specialized Python-based toolkit designed for large-scale single-cell RNA-seq data analysis built on the AnnData structure. This skill enables Claude to guide users through the entire bioinformatics pipeline, from loading 10X Genomics or h5ad data to performing quality control, dimensionality reduction via UMAP or t-SNE, and identifying marker genes for cell type annotation. It provides pre-configured scripts for automated QC and publication-quality visualizations, making it an essential resource for bioinformaticians and researchers needing robust, reproducible analysis patterns.