Note that CellAssign could be labeled with Not run
#249
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sjspielman
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Jan 22, 2024
Co-authored-by: Stephanie Spielman <[email protected]>
sjspielman
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Jan 22, 2024
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| | `cellassign_predictions` | If cell typing with `CellAssign` was performed and completed successfully, the full matrix of predictions across cells and cell types | | ||
| | `cellassign_reference` | If cell typing with `CellAssign` was performed and completed successfully, the reference name as established by the Data Lab used for cell type annotation | | ||
| | `cellassign_reference_organs` | If cell typing with `CellAssign` was performed and completed successfully, a comma-separated list of organs and/or tissue compartments from which marker genes were obtained to create the reference | | ||
| | `cellassign_reference_source` | If cell typing with `CellAssign` was performed and completed successfully, the source of the reference dataset (default is [`PanglaoDB`](https://panglaodb.se/)) | | ||
| | `cellassign_reference_version` | If cell typing with `CellAssign` was performed and completed successfully, the version of the reference dataset source. For references obtained from `PanglaoDB`, the version scheme is a date in ISO8601 format | |
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@sjspielman I like the wording you suggested for the max prediction score. I also used that same wording for any of the metadata slots related to |
allyhawkins
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Jan 22, 2024
…-run Note that CellAssign could be labeled with `Not run`
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In AlexsLemonade/scpca-nf#662, we accounted for processed objects that do not successfully complete CellAssign due to low numbers of cells. There, we still include the
cellassign_celltype_annotationcolumn, but we populate it withNot run. I think I noted both areas where this column is mentioned to include theNot runoption.