HoloFoodR
Bioc currentR interface to EBI HoloFood resource
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
52 5 exported
Complexity
4.3 avg / 53 max
Call network
52 nodes / 72 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
4,185
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
47
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
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
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 6includes a package overview page
- Examples that run
- 80%4 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- HoloFoodR HTML
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/ebi-metagenomics/holofoodr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| analysis_ids | vector | 52 elements | No other package |
| mae_metagenomic | – | – | – |
| salmon_mae_without_mgnify | – | – | – |
| salmon_metagenomic_tse | – | – | – |
Topics
People
- Tuomas Borman author maintainer
- Leo Lahti author
- Artur Sannikov author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HoloFoodR")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.