qmtools
Bioc currentQuantitative Metabolomics Data Processing Tools
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
63 18 exported
Complexity
4.2 avg / 70 max
Call network
63 nodes / 54 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
5,609
Files
59
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
22
Internal functions
44
Testing
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (1 internal)includes a package overview page
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 67%
Repository practices
Checks run against github.com/himesgroup/qmtools on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
Topics
People
- Jaehyun Joo author maintainer
- Blanca Himes author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("qmtools")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.