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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Add "Unclassified cell" to documentation #333

Closed sjspielman closed 3 months ago

sjspielman commented 3 months ago

A question has come up about cell type annotations in OpenScPCA, and it turns out we are missing some docs here! We use "Unclassified cell" labels for cells that do not get run through cell typing, but this is not documented anywhere. We should note this both in the cell type annotation section and in the SCE contents section.

Relevant code is in this scpca-nf script: https://github.com/AlexsLemonade/scpca-nf/blob/main/bin/add_celltypes_to_sce.R

sjspielman commented 3 months ago

Noting our "docs" in the cell type report: https://github.com/AlexsLemonade/scpca-nf/blob/f215046b3a9d9ddc50fac1a198a57e1bb813aeae/templates/qc_report/celltypes_qc.rmd#L342-L344

sjspielman commented 3 months ago

closed by #335