MGnifyR
Bioc currentR interface to EBI MGnify metagenomics resource
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
45 11 exported
Complexity
5.5 avg / 25 max
Call network
45 nodes / 51 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
5,613
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
32
Internal functions
34
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
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
Artistic-2.0 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
175 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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (1)
Bioconductor (1)
People
- Tuomas Borman author maintainer
- Ben Allen author
- Leo Lahti author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MGnifyR")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.