API

Table of Contents

Prediction & Thresholding

• PredictCellCycle
  Run the ccAFv2 classifier and assign cell cycle states.
• AdjustCellCycleThreshold
  Re-assign states based on a new prediction confidence threshold.

Data Preparation For Cell Cycle Regression

• PrepareForCellCycleRegression
  Compute module scores from marker gene sets for regression.

Visualization

• DimPlot.ccAFv2
  Plot predicted cell cycle states on a UMAP or PCA.
• SpatialDimPlot.ccAFv2
  Visualize predicted states in spatial transcriptomics data.
• ThresholdPlot
  Visualize how prediction thresholds affect state assignment.