single-cell-annotation-guide

For single-cell RNA-seq cell type annotation, you should choose between manual marker-based inspection, automated tools like CellTypist, or reference-based label transfer using popV. This guide provides a decision framework to help you select the right strategy based on your dataset and research question.

To decide between manual marker-based and automated cell annotation for scRNA-seq, evaluate your data complexity and research goals. This guide details the use cases, common pitfalls, and workflow steps for manual inspection versus automated methods like CellTypist to inform your choice.

Yes, you can use a reference atlas like the Human Cell Atlas for label transfer in scRNA-seq. This guide covers reference-based annotation strategies using popV, detailing when to apply them and how to integrate reference atlases into your workflow for robust cell type identification.

Common pitfalls during cell type annotation in single-cell RNA-seq analysis include misinterpreting marker genes and misapplying automated models. This guide details these common errors and provides actionable best practices to avoid them, ensuring robust and accurate annotation results.

You should not use automated tools like CellTypist for scRNA-seq cell annotation when your dataset contains novel or rare cell populations not represented in existing models. This guide helps you identify these constraints and switch to manual marker-based strategies to avoid inaccurate label transfers.