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Score cell cycle phases
CellCycleScoring(object, g2m.genes, s.genes, set.ident = FALSE)
A Seurat object
A vector of genes associated with G2M phase
A vector of genes associated with S phases
If true, sets identity to phase assignments Stashes old identities in 'old.ident'
A Seurat object with the following columns added to object@meta.data: S.Score, G2M.Score, and Phase
AddModuleScore
# NOT RUN {
# pbmc_small doesn't have any cell-cycle genes
# To run CellCycleScoring, please use a dataset with cell-cycle genes
# An example is available at http://satijalab.org/seurat/cell_cycle_vignette.html
pbmc_small <- CellCycleScoring(
object = pbmc_small,
g2m.genes = cc.genes$g2m.genes,
s.genes = cc.genes$s.genes
)
head(x = pbmc_small@meta.data)
# }
# NOT RUN {
# }
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