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Single sample within group #67

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RunyuXia opened this issue Jan 12, 2025 · 1 comment
Open

Single sample within group #67

RunyuXia opened this issue Jan 12, 2025 · 1 comment
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enhancement New feature or request

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@RunyuXia
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Description of feature

Hi! I have two Visium HD samples, one belongs to the disease phenotype and the other one wild type. I was wondering if it’s possible to use CellCharter to compare the spatial niches between these two samples? Thank you for your help!
@RunyuXia RunyuXia added the enhancement New feature or request label Jan 12, 2025
@marcovarrone
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Hi @RunyuXia, absolutely!

If you managed to load the Visium HD dataset in anndata format, you can follow the same steps shown in the CosMx tutorial. The procedure should be the same.

In that tutorial, I compute niches for multiple samples, as it is in your case.

Let me know if you have any trouble in running CellCharter on your samples :)

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@marcovarrone @RunyuXia