MetaboDynamics
Bioc currentBayesian analysis of longitudinal metabolomics data
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
MetaboDynamics is an R-package that provides a framework of probabilistic models to analyze longitudinal metabolomics data. It enables robust estimation of mean concentrations despite varying spread between timepoints and reports differences between timepoints as well as metabolite specific dynamics profiles that can be used for identifying "dynamics clusters" of metabolites of similar dynamics. Provides probabilistic over-representation analysis of KEGG functional modules and pathways as well as comparison between clusters of different experimental conditions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 15 exported
Complexity
10.2 avg / 23 max
Call network
22 nodes / 5 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
6,584
Files
89
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
23.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
1 externalGNU make
C++ standard
C++17
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-05-24
Latest release
2026-09-07
Avg cadence
236 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
- Help pages
- 28 (8 internal)includes a package overview page
- Examples that run
- 100%15 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/katjadanielzik/metabodynamics on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| IDs | spec_tbl_df | 98 × 2 | No other package |
| longitudinalMetabolomics | – | – | – |
| longitudinalMetabolomics_df | tibble | 2,352 × 8 | No other package |
| metabolite_modules | spec_tbl_df | 348 × 8 | No other package |
| modules_compounds | data.frame | 3,242 × 6 | No other package |
Topics
People
- Katja Danielzik author maintainer
- Daniel Hoffmann contributor
- Simo Kitanovski contributor
- Johann Matschke contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MetaboDynamics")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
The repository also keeps a CITATION.cff.
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.