Here are some skills about the best practices for analyzing the single-cell/Spatial Omics data. When you need to do the specific analysis tasks described in this file, you can load the related skill files linked here to help you.

Skills for querying and downloading data from genomic, transcriptomic, and single-cell databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, and large-scale single-cell data.

Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.

Skills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.

Skills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.

This directory contains bioinformatics upstream analysis skills for agent-assisted data processing. Each skill provides workflow guidance, code templates, and best practices for specific analysis types.