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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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cellcall with integrated data (Seurat) #28

Open akramdi opened 2 years ago

akramdi commented 2 years ago

Hello,

Could you give us some indications on how to create the right input data for cellcall in case of integrated data (Seurat)? We plan to extract expression data from the "counts" slots of the "SCT" assay, does this sound reasonable ?

Many thanks fot the help,

ShellyCoder commented 2 years ago

Apologize for a late reply. If you want to extract count data of _endothelialcell from the seurat object "_seuratobj". The example code has followed:

yourDF <- as.matrix(GetAssayData(seurat_obj, slot = "counts")[, WhichCells(seurat_obj, ident = "endothelial_cell")])