# pbmcMultiome.SeuratData_0.1.1 pbmc3k.SeuratData_3.1.4 # ssHippo.SeuratData_3.1.4 pbmcsca.SeuratData_3.0.0 # stats graphics grDevices utils datasets methods base # LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C # LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 # BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so As an example, we’re going to select the same set of cells as before, and set their identity class to “selected” This is done by passing the Seurat object used to make the plot into CellSelector(), as well as an identity class. In addition to returning a vector of cell names, CellSelector() can also take the selected cells and assign a new identity to them, returning a Seurat object with the identity classes already set. Using CellSelector to Automatically Assign Cell Identities Only.pos = TRUE ) head ( newcells.markers ) # p_val avg_log2FC pct.1 pct.2 p_val_adj Idents ( pbmc3k.final, cells = select.cells ) <- "NewCells" # Now, we find markers that are specific to the new cells, and find clear DC markers newcells.markers <- FindMarkers ( pbmc3k.final, ident.1 = "NewCells", ident.2 = "CD14+ Mono", = 0.3,
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