InTAD
Bioc currentSearch for correlation between epigenetic signals and gene expression in TADs
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 9 exported
Complexity
6.8 avg / 13 max
Call network
13 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
2,623
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
12
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.23
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
3.5
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
Konstantin Okonechnikov
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("InTAD")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.