Run cell cycle scoring — RunCellCycle • scop

Estimate cell cycle state with Seurat gene-set scoring, scran::cyclone(), or tricycle.

Usage

RunCellCycle(
  srt,
  method = c("Seurat", "cyclone", "tricycle"),
  assay = NULL,
  layer = "counts",
  species = "Homo_sapiens",
  name = "CellCycle",
  phase_col = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

srt: A Seurat object.
method: Cell cycle estimation method. One of "Seurat", "cyclone", or "tricycle".
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
layer: Data layer used by cyclone and tricycle. Default is "counts".
species: Latin names for animals, i.e., "Homo_sapiens", "Mus_musculus"
name: Prefix for metadata columns and tricycle reduction names. Default is "CellCycle".
phase_col: Optional metadata column used to store the final phase call, for example "Phase". Default is NULL, which avoids writing a compatibility phase column.
overwrite: Whether to overwrite existing output columns. Default is FALSE.
verbose: Whether to print the message. Default is TRUE.
...: Additional arguments passed to the selected method.

Value

A Seurat object with cell cycle metadata and, for tricycle, a tricycle embedding reduction.

Examples

data(pancreas_sub)
srt <- pancreas_sub[, 1:80]

if (requireNamespace("scran", quietly = TRUE)) {
  srt <- RunCellCycle(
    srt,
    method = "cyclone",
    species = "Mus_musculus",
    name = "Cyclone"
  )
}
#> ℹ [2026-05-14 06:55:42] Start cell cycle scoring
#> 'select()' returned 1:many mapping between keys and columns
#> ℹ [2026-05-14 06:55:43] Map input feature names to ENSEMBL IDs with org.Mm.eg.db for scran::cyclone
#> ✔ [2026-05-14 06:55:53] Cell cycle scoring completed

if (requireNamespace("tricycle", quietly = TRUE)) {
  srt <- RunCellCycle(
    srt,
    method = "tricycle",
    species = "Mus_musculus",
    name = "Tricycle"
  )
  if ("Cyclone_cyclone_Phase" %in% colnames(srt@meta.data)) {
    CellDimPlot(
      srt,
      reduction = "Tricycle_tricycleEmbedding",
      group.by = "Cyclone_cyclone_Phase"
    )
  }
  FeatureDimPlot(
    srt,
    reduction = "Tricycle_tricycleEmbedding",
    features = "Tricycle_tricyclePosition"
  )
}
#> ℹ [2026-05-14 06:55:53] Start cell cycle scoring
#> Warning: Layer ‘data’ is empty
#> Warning: Layer ‘scale.data’ is empty
#> Warning: 'librarySizeFactors' is deprecated.
#> Use 'scrapper::centerSizeFactors' instead.
#> See help("Deprecated")
#> Warning: 'normalizeCounts' is deprecated.
#> Use 'scrapper::normalizeCounts' instead.
#> See help("Deprecated")
#> No custom reference projection matrix provided. The ref learned from mouse Neuroshpere data will be used.
#> The number of projection genes found in the new data is 485.
#> ✔ [2026-05-14 06:56:18] Cell cycle scoring completed