TSCAN
Bioc currentTools for Single-Cell Analysis
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 9 exported
Complexity
4.2 avg / 14 max
Call network
17 nodes / 2 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
3,020
Files
54
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
8
Testing
Has tests
Yes
Test-to-code ratio
0.40
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL(>=2)
License flags
not SPDX, not OSI
History
Versions
24
First release
2014-10-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 17 (1 internal)includes a package overview page
- Examples that run
- 93%13 run in a plain check · 1 never run
- Exported functions with examples
- 93%
- Documented parameters
- 88%
- Return-value docs
- 87%
- Help pages citing references
- 35%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| lpsdata | matrix | 16,776 × 131 | No other package |
Topics
Depended on by (6)
Bioconductor (5)
CRAN (1)
Suggested by (1)
People
- Zhicheng Ji author maintainer
- Hongkai Ji author
- Aaron Lun contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("TSCAN")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.