DOI: 10.18129/B9.bioc.tricycle  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tricycle.

tricycle: Transferable Representation and Inference of cell cycle

Bioconductor version: 3.16

The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

Author: Shijie Zheng [aut, cre]

Maintainer: Shijie Zheng <shijieczheng at>

Citation (from within R, enter citation("tricycle")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script tricycle: Transferable Representation and Inference of Cell Cycle
PDF   Reference Manual
Text   NEWS


biocViews BiologicalQuestion, DimensionReduction, ImmunoOncology, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.0), SingleCellExperiment
Imports methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils
Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat,,
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tricycle_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) tricycle_1.6.0.tgz
macOS Binary (arm64) tricycle_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: