tricycle
Bioc currenttricycle: Transferable Representation and Inference of cell cycle
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 9 exported
Complexity
4.4 avg / 15 max
Call network
19 nodes / 15 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,437
Files
40
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
10
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 42%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/hansenlab/tricycle on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2021-04-05 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RevelioGeneList | list | 5 elements | No other package |
| neuroRef | data.frame | 500 × 5 | No other package |
| neurosphere_example | – | – | – |
Topics
People
- Shijie Zheng author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("tricycle")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-021-02581-y.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.