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Getting marker genes for cell types

Hi,

I'm currently drawing a umap plot through python scanpy

While, doing so I get clusters that needs to be annotated. So, I used packages such as the celltypist which helps me annotate automatically.

However, using automatic annotation through celltypist, does not give the certain cell types that I am interested in. So, I would like to look for only certain cell types instead of the pretrained(ordered) models from celltypist.

For example, I would like to plot or view only for 'fibroblasts', 'T cells', and 'Epithelial cells'.

Is there a way to find marker genes for the selected cell types?

clustering marker-genes umap
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written by orzrzlyo • orzrzlyo

1 answer

It seems strange that celltypist would not identify these major cell classes -- you should double check your data quality. For the marker lists, you can use the Azimuth or CellMarker gene sets, both available on EnrichR (https://maayanlab.cloud/Enrichr/#libraries)

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written by LChart LChart

Thank you! Also, cell typist would successfully identify the above cell types, however, they seemed to be in a pretrained or pre-organized under the name of a model. Though the typical cells that I want are from different models. For example one cell from "Healthy_Human_Liver" the model and one cell from the "Fetal_Human_Skin" model.

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written by orzrzlyo • orzrzlyo

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