sc-best-practices-complete-100percent

What problem does it solve?

This skill consolidates the sc-best-practices-complete-100percent documentation to guide researchers through robust, end-to-end single-cell analysis workflows, from preprocessing to advanced differential abundance methods.

Core Features & Use Cases

• Comprehensive guidance: Covers preprocessing, compositional analysis, differential abundance testing (e.g., scCODA, Tasccoda, DA testing), and visualization across scRNA-seq, spatial transcriptomics, and multi-omics contexts.
• Real-world references: Integrates exemplar analyses and case studies (e.g., Haber dataset) to demonstrate practical workflows and interpretations.
• Use Case: A researcher applying compositional analysis to compare cell-type abundances across conditions can follow structured pipelines and load relevant references to reproduce established results.

Quick Start

Start by reading the SKILL.md frontmatter to understand the skill scope and then consult references/index.md for an overview of topics and available guidance.