cliqueMS
Bioc currentAnnotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.GuimerĂ and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
55 4 exported
Complexity
2.2 avg / 6 max
Call network
55 nodes / 31 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
4,304
Files
47
Compiled share
40.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
18
Internal functions
23
Testing
Has tests
Yes
Test-to-code ratio
0.07
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
25%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
1 externalC++11
C++ standard
C++11
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2020-03-26
Latest release
2026-04-28
Avg cadence
172 days
Cold removal rate
–
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
- 12includes a package overview page
- Examples that run
- 100%8 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/osenan/cliquems on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ex.cliqueGroups | – | – | – |
| negative.adinfo | data.frame | 11 × 5 | 2 packages |
| positive.adinfo | data.frame | 39 × 5 | 2 packages |
Topics
People
- Oriol Senan Campos author maintainer
- Antoni Aguilar-Mogas author
- Jordi Capellades author
- Roger Guimera author
- Miriam Navarro author
- Marta Sales-Pardo author
- Oscar Yanes author
Cite
Cite this package
Run in R for the authors' entry:
citation("cliqueMS")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btz207.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.