Tag: WNN

WNN in Seurat

Dear all, I am trying to follow the WNN vignette here satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html After the steps below, I would like to annotate my clusters, hence I need to know the markers which best represent each cluster. pbmc <- FindMultiModalNeighbors(pbmc, reduction.list = list(“pca”, “lsi”), dims.list = list(1:50, 2:50)) pbmc <- RunUMAP(pbmc, nn.name

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WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data

WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data 0 I want to build a UMAP from CITE-seq data with a joint embedding of the scRNA-seq and protein ab data. What’s the ‘best’ method in terms of representing the most accurate embedding? In the totalVI paper, they say totalVI >…

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