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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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cell type information #2

Closed BenxiaHu closed 3 years ago

BenxiaHu commented 3 years ago

Hello, when I try to run scDaPars on one public scRNA-seq, I reaslized that I need to provide the cell type information. scDaPars.res.umap = umap(t(scDaPars.res)) scDaPars.res.umap.data = data.frame(scDaPars.res.umap$layout) colnames(scDaPars.res.umap.data) = c("Dim1", "Dim2") scDaPars.res.umap.data$cellType = cell_type$source_name

My question is that scDaPars can identify cell clusters, not depends known cell typ information?

YiPeng-Gao commented 3 years ago

Hello, when I try to run scDaPars on one public scRNA-seq, I reaslized that I need to provide the cell type information. scDaPars.res.umap = umap(t(scDaPars.res)) scDaPars.res.umap.data = data.frame(scDaPars.res.umap$layout) colnames(scDaPars.res.umap.data) = c("Dim1", "Dim2") scDaPars.res.umap.data$cellType = cell_type$source_name

My question is that scDaPars can identify cell clusters, not depends known cell typ information?

The cell type information is used as ground truth to evaluate if the clustering result is correct. The clustering itself does not require any prior cell type information.

BenxiaHu commented 3 years ago

great.