gatom
Bioc currentFinding an Active Metabolic Module in Atom Transition Network
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
73 15 exported
Complexity
2.9 avg / 12 max
Call network
73 nodes / 68 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
4,240
Files
63
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
58
Testing & CI
Has tests
Yes
Test-to-code ratio
0.24
testthat edition
–
CI present
Yes
CI type
["github-actions","travis"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
5.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
MIT + file LICENCE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
Latest release
2026-06-23
Avg cadence
189 days
Cold removal rate
–
Dep drift
4
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
- 87%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Alexey Sergushichev author maintainer
- Mariia Emelianova author
- Anastasiia Gainullina author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("gatom")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.