structToolbox
Bioc currentData processing & analysis tools for Metabolomics and other omics
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). Ontology terms have been integrated to provide standardised definitions for the different methods, inputs and outputs.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
136 110 exported
Complexity
1.3 avg / 9 max
Call network
136 nodes / 9 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
23,608
Files
263
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
111
Internal functions
26
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-05-26
Latest release
2026-04-28
Avg cadence
185 days
Cold removal rate
100%
Dep drift
5
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
- 100%
- Return-value docs
- 100%
- References docs
- 29%
Topics
Depended on by (2)
Bioconductor (2)
People
- Gavin Rhys Lloyd author maintainer
- Ralf Johannes Maria Weber author