Uses scran::cyclone()
to assign cell-cycle phases to each cell.
Assignments are available in colData
in the cell_cycle
slot.
calc_cell_cycle(fsce, expt = "rnaseq", org = "human", ...)
fsce | |
---|---|
expt | Data to use for calculating variable features
(default is |
org | organism for gene pairs, human or mouse |
... | additional params for |
Scialdone A, Natarajana KN, Saraiva LR et al. (2015). Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85:54--61
# \donttest{ fsce_small <- calc_cell_cycle(fsce_small) SingleCellExperiment::colData(fsce_small[["rnaseq"]])#> DataFrame with 250 rows and 4 columns #> cell_id k_cluster leiden_cluster cell_cycle #> <character> <character> <character> <character> #> TGCGGGTGTAGAGTGC TGCGGGTGTAGAGTGC 2 2 S #> TGGTTCCCATCTATGG TGGTTCCCATCTATGG 6 4 S #> CATATTCCACGTCAGC CATATTCCACGTCAGC 2 2 G2M #> TCACAAGTCCTGCTTG TCACAAGTCCTGCTTG 5 3 G1 #> GGAATAATCCAGGGCT GGAATAATCCAGGGCT 4 4 G1 #> ... ... ... ... ... #> CTACGTCCACCACGTG CTACGTCCACCACGTG 6 4 G1 #> TGTGGTAAGGTGCTTT TGTGGTAAGGTGCTTT 3 6 G1 #> AGCGTCGGTCGAGTTT AGCGTCGGTCGAGTTT 3 6 G1 #> CTCGAAAAGTTCGATC CTCGAAAAGTTCGATC 6 5 G2M #> TGACAACGTCGCATAT TGACAACGTCGCATAT 6 4 S# }