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NathanSkene / EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
https://nathanskene.github.io/EWCE/index.html
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How do I analyze a Seurat object? #94

Closed jmzhang1911 closed 3 months ago

jmzhang1911 commented 3 months ago

Thank you for developing such an excellent tool! I'm curious about how to directly analyze a Seurat object. Looking forward to your reply!

NathanSkene commented 3 months ago

You just need to find the matrix within the Seurat object that represents gene expression, and follow the tutorial for creating a CTD

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Thank you for developing such an excellent tool! I'm curious about how to directly analyze a Seurat object. Looking forward to your reply!

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bschilder commented 3 months ago

@jmzhang1911 Seurat has a function to convert Seurat objects to SingleCellExperiment format: Seurat::as.SingleCellExperiment

SingleCellExperiment objects can then be used as input to EWCE::generate_celltype_data to generate your CTD reference for EWCE analyses.