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Label-free mode? #303

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amoore-vm opened this issue Jan 30, 2025 · 0 comments
Open

Label-free mode? #303

amoore-vm opened this issue Jan 30, 2025 · 0 comments

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@amoore-vm
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In the CellChat publication and documentation, it mentions a label-free model: "CellChat requires two user inputs: one is the gene expression data of cells, and the other is either user assigned cell labels (i.e., label-based mode) or a low-dimensional representation of the single-cell data (i.e., label-free mode). For the latter, CellChat automatically groups cells by building a shared neighbor graph based on the cell-cell distance in the low-dimensional space or the pseudotemporal trajectory space. "

We are getting poor results on Xenium data (20 ligand-receptor pairs). We would like to try using the label-free mode, but the tutorial assumes you will provide labeled data. How do you run label-free mode?

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