single-cell-annotation

# 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, stressed) overlaid on a cell type. Annotation should target cell types first; states are attributes that may further subdivide a type but should not be conflated with type identity. ### Marker Genes and Marker Panels Marker genes are genes whose expression is enriched in a specific cell...