# tricycle: Transferable Representation and Inference of cell cycle

## Documentation for package ‘tricycle’ version 1.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

circle_scale_legend | Get the cyclic legend
diagnose_totalumi | Diagnostic function for UMI based datasets
estimate_cycle_position | Assign cell cycle position
estimate_Schwabe_stage | Assign cell cycle stages using Schwabe method
fit_periodic_loess | Fit periodic loess line with circular predictor
neuroRef | Pre-learned reference projection matrix from the Neurosphere dataset
neurosphere_example | Example SingleCellExperiment dataset
plot_ccposition_den | Plot cell cycle position kernel density stratified by a factor
plot_emb_circle_scale | Plot embedding with cyclic cell cycle position
project_cycle_space | Project data into the cell cycle pattern space
RevelioGeneList | 5 stage cell cycle gene marker list from Revelio
run_pca_cc_genes | Run PCA on Gene Ontology cell cycle genes