Cell Annotation
Platform

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snRNA-seq of human optic nerve and optic nerve head - all cells

Main

Cell Metadata

Ontology Term: macrophageCL:0000235
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: macrophage VCAN+
Category Class of which the cell type is a subclass.: mononuclear phagocyteCL:0000113
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD163, VCAN
Canonical Marker Genes: CD163, VCAN
Rationale: A macrophage sub class that expresses CD163 and VCAN
Rationale DOI: https://doi.org/10.1073/pnas.2306153120

Set of Labels Description: We used scVI for data integration and then manually annotated each cell cluster based on marker gene expression
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: scvi-tools 1.3.0
Algorithm URL: https://github.com/scverse/scvi-tools