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markers-annotation

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Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seurat (R). Use when finding genes that distinguish clusters, ranking markers for annotation, scoring gene signatures, hand-labeling clusters, or deciding between Wilcoxon marker ranking and pseudobulk condition DE.

When to use

• finding genes that distinguish clusters
• ranking markers for annotation
• scoring gene signatures
• hand-labeling clusters
• deciding between Wilcoxon marker ranking and pseudobulk condition DE

When not to use

• automated reference-based label transfer
• SingleR
• CellTypist
• Azimuth
• scANVI
• cross-condition compositional change
• differential abundance

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