geomeTriD
Bioc currentA R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based 'three.js' (https://threejs.org/) or the rgl rendering library. It is designed to identify and explore spatial chromatin patterns within genomic regions. The package generates dynamic 3D plots and HTML widgets that integrate seamlessly with Shiny applications, enabling researchers to visualize chromatin organization, detect spatial features, and compare structural dynamics across different conditions and data types.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
125 28 exported
Complexity
5 avg / 48 max
Call network
125 nodes / 160 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
8,921
Files
78
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
29
Internal functions
97
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2025-01-03
Latest release
2026-04-28
Avg cadence
155 days
Cold removal rate
–
Dep drift
10
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
- 79%
- Return-value docs
- 91%
- References docs
- 0%
Topics
People
- Jianhong Ou author maintainer
- Kenneth Poss author fnd
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("geomeTriD")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
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.