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.
None published for Bioconductor
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
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
12
Internal functions
4
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.23
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
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
- Help pages
- 23
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 83%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| enhSel | data.frame | 116 × 25 | No other package |
| enhSelGR | – | – | – |
| loopsDfSel | data.frame | 285 × 10 | No other package |
| mbAnnData | data.frame | 25 × 5 | No other package |
| rpkmCountsSel | data.frame | 2,080 × 25 | No other package |
| tadGR | – | – | – |
| txsSel | – | – | – |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("InTAD")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-019-2655-2.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.