single-cell-annotation
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
npx skills add BioTender-max/awesome-bio-agent-skills --skill single-cell-annotation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single Cell RNA-seq Cell Type Annotation --- ## Metadata **Short Description**: Best practices for annotating cell types in single-cell RNA-seq data using marker-based, automated, and reference-based approaches. **Authors**: Distilled from "Single-cell best practices" by Luecken, M.D. et al. **Affiliations**: Helmholtz Munich, Wellcome Sanger Institute, Harvard Medical School, and contributors **Version**: 1.0 **Last Updated**: January 2025 **License**: CC BY 4.0 **Commercial Use**: ✅ Allowed **Source**: https://www.sc-best-practices.org/cellular_structure/annotation.html **Citation**: Luecken, M.D., Theis, F.J. et al. (2023). Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology. --- ## Overview Cell type annotation is the process of assigning cell type labels to clusters or individual cells in single-cell RNA-seq data. This guide covers three main approaches and their practical implementation. ## Key Concepts ### Cell Type vs. Cell State A **cell type** is a stable identity defined by a developmental trajectory and core marker gene program (e.g., CD4+ T cell, hepatocyte). A **cell state** is a transient condition (activated, cycling, stre
- Metadata
- Overview
- Key Concepts
- Cell Type vs. Cell State
- Marker Genes and Marker Panels
- Reference Atlases and Label Transfer
- Decision Framework
- Decision Table
- Three Annotation Approaches
- 1. Manual Marker-Based Annotation
- 2. Automated Annotation
- 3. Reference-Based Label Transfer
- Recommended Workflow
- Step 1: Quality Control First
What does the single-cell-annotation skill do?
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill single-cell-annotation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.