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Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
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CellTypist_Immune_Reference_v2 question #103

Closed NikicaJEa closed 6 months ago

NikicaJEa commented 6 months ago

Hi! I was playing around with celltypist and wanted to test different training parameters on the most recent reference dataset immune_v2. I saw in your wiki that you have a prepared file (/nfs/team205/cx1/Celltypist/expand_immune/data/CellTypist_Immune_Reference_v2.h5ad) which is unfortunately not publicly available. Therefore I tried to reconstruct the immune_v2 reference dataset by combining the organ atlas datasets.

However, there I encountered a small issue. I noticed that the annotation in Blood.h5ad does not contain the new immune_v2 annotation but probably the outdated version? For example Tgd_CRTAM+ can be found in the label harmonization tree but not in the Curated_annotation slot of Blood.h5ad .

Any help is much appreciated! Cheers!

ChuanXu1 commented 6 months ago

@NikicaJEa, the reference data is here https://cog.sanger.ac.uk/celltypist/rm/CellTypist_Immune_Reference_v2_count.h5ad

NikicaJEa commented 6 months ago

Thank you so much!