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cell-annotation

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Automated reference-based cell type annotation for single-cell RNA-seq using CellTypist, SingleR, Azimuth, scANVI, and scmap to transfer labels from a reference. Use when annotating cell types from a reference atlas or pretrained model, transferring labels onto a query, assessing prediction confidence and rejection, or triaging whether an unexpected cluster is a novel type versus a doublet, low-quality, or batch artifact.

When to use

• annotating cell types from a reference atlas
• transferring labels onto a query
• assessing prediction confidence and rejection
• triaging unexpected clusters
• identifying doublets, low-quality, or batch artifacts
• using CellTypist, SingleR, Azimuth, scANVI, or scmap

When not to use

• manual marker discovery
• hand-labeling

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