SC Best Practices Skills Index

npx skills add BioTender-max/awesome-bio-agent-skills --skill sc_best_practices --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# SC Best Practices Skills Best practices and workflows for single-cell and spatial omics data analysis, based on the [Single-cell Best Practices](https://www.sc-best-practices.org) book. When performing specific analysis tasks, load the relevant skill files to guide your approach. ## Available Skills ### Introduction & Fundamentals Overview of single-cell RNA-seq technologies, raw data processing pipelines, analysis frameworks, and data format interoperability. **Skill file**: [introduction.md](./introduction.md) **When to use**: - Starting a new single-cell project and choosing technology/tools - Need guidance on raw data processing (CellRanger, STARsolo, Kallisto) - Converting between AnnData, SingleCellExperiment, and Seurat formats --- ### Preprocessing & Quality Control Quality control, ambient RNA removal, doublet detection, normalization, feature selection, and dimensionality reduction. **Skill file**: [preprocessing.md](./preprocessing.md) **When to use**: - Starting analysis of a new single-cell dataset - Filtering low-quality cells with MAD-based thresholds - Choosing normalization and feature selection methods - Running PCA, UMAP, or t-SNE --- ### Clustering & Cell Type