TreeSummarizedExperiment
Bioc currentTreeSummarizedExperiment: a S4 Class for Data with Tree Structures
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
73 31 exported
Complexity
3.9 avg / 19 max
Call network
73 nodes / 75 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
9,727
Files
123
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
45
Internal functions
42
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.28
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
15
First release
2019-06-03
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 55 (20 internal)includes a package overview page
- Examples that run
- 91%29 run in a plain check · 3 never run
- Exported functions with examples
- 97%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- 1. Introduction to TreeSE HTML
- 2. Combine TSEs HTML
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 |
|---|---|---|---|
| tinyTree | phylo | 5 elements | No other package |
Topics
Depended on by (23)
Show all 34 packagesHide all 34 packages
Bioconductor (22)
CRAN (1)
People
- Ruizhu Huang author maintainer
- Tuomas Borman contributor
- Felix G.M. Ernst contributor
- Mark Robinson contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("TreeSummarizedExperiment")The package provides a citation file, so citation() returns the authors' own entry.
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.