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Markers listed in Azimuth for human tonsil are incorrect and in conflict with original preprint? #198

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denvercal1234GitHub opened this issue Jan 4, 2024 · 0 comments

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@denvercal1234GitHub
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denvercal1234GitHub commented Jan 4, 2024

Hi there,

Thanks for the tool.

The markers listed for the celltype.l2 at https://azimuth.hubmapconsortium.org/references/#Human%20-%20Tonsil for the human tonsil reference dataset are not correct and are entirely different from what detailed in the preprint or through the author's HCATonsilData tool developed by @massonix

EX: For CM CD8 T cells:

  • From HCATonsilData tool: IL7R,ANXA1,S100A4,CCR7,CD28
  • From Azimuth app/website: CD2, CD8A, CD8B, GPR171, IL7R, ITGA1, GZMK, GZMA, SAMD3, GIMAP7

Would you mind clarifying whether the list is just not updated but the annotation is still using the correct markers?

Thank you.

@denvercal1234GitHub denvercal1234GitHub changed the title Markers listed in Azimuth for human tonsil are incorrect and in conflict with original preprints? Markers listed in Azimuth for human tonsil are incorrect and in conflict with original preprint? Jan 4, 2024
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