SpectralTAD
Bioc currentSpectralTAD: Hierarchical TAD detection using spectral clustering
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4 2 exported
Complexity
15 avg / 29 max
Call network
4 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
1,467
Files
40
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
2
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.01
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
3.6
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-08-20
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 3
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- SpectralTAD HTML
- Remove remaining PRIMME references
From NEWS in the release
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/dozmorovlab/spectraltad on 2026-10-25.
GitHub Pages site last deployed 2026-08-21
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| rao_chr20_25_rep | data.frame | 2,125,980 × 3 | No other package |
Topics
Suggested by (1)
People
- Mikhail Dozmorov author maintainer
- Kellen Cresswell author
- John Stansfield author
Cite
Cite this package
Run in R for the authors' entry:
citation("SpectralTAD")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-020-03652-w.
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.