TENET
Bioc currentR package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
TENET identifies key transcription factors (TFs) and regulatory elements (REs) linked to a specific cell type by finding significantly correlated differences in gene expression and RE DNA methylation between case and control input datasets, and identifying the top genes by number of significant RE DNA methylation site links. It also includes many tools for visualization and analysis of the results, including plots displaying and comparing methylation and expression data and methylation site link counts, survival analysis, TF motif searching in the vicinity of linked RE DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser track file generation. A utility function is also provided to download methylation, expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use in TENET or other analyses.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
92 23 exported
Complexity
6.1 avg / 116 max
Call network
92 nodes / 209 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
19,346
Files
64
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
69
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
3.2%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-05-06
Latest release
2026-04-28
Avg cadence
179 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 26 (1 internal)includes a package overview page
- Examples that run
- 100%25 run in a plain check (22 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Using TENET HTML
Repository practices
Checks run against github.com/rhielab/tenet on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| humanTranscriptionFactorDb | data.frame | 2,765 × 28 | No other package |
| humanTranscriptionFactorList | vector | 1,639 elements | No other package |
Topics
Available on
Suggested by (2)
People
- Rhie Lab at the University of Southern California maintainer
- Daniel Mullen author
- Ethan Nelson-Moore author
- Suhn Rhie author
- Zexun Wu author
Cite
Cite this package
Run in R for the authors' entry:
citation("TENET")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btaf435.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.