omXplore
Bioc currentVizualization tools for 'omics' datasets with R
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
104 100 exported
Complexity
3.5 avg / 45 max
Call network
104 nodes / 117 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
39,511
Files
155
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
100
Internal functions
4
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
3.29
testthat edition
–
Docs
Roxygen coverage
99%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
3
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2025-03-04
Latest release
2026-04-28
Avg cadence
160 days
Cold removal rate
100%
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
- 29 (2 internal)
- Examples that run
- 100%27 run in a plain check (16 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 85%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Adding third party plots HTML
- omXplore HTML
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/edyp-lab/omxplore on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-08-06 · The repository has a site deploy workflow
Datasets
Topics
People
- Samuel Wieczorek author maintainer
- Cyril Ariztegui contributor
- Thomas Burger author
- Enora Fremy contributor
- Manon Gaudin contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("omXplore")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.