curatedMetagenomicData
Bioc currentCurated Metagenomic Data of the Human Microbiome
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
3 3 exported
Complexity
8 avg / 13 max
Call network
3 nodes / 2 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
3,607
Files
32
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
0
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.49
testthat edition
–
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
4.1.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-12-12
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 5 (1 internal)
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
11 development-tooling and community-health practices detected across 6 families in the upstream repository
Checks run against github.com/waldronlab/curatedmetagenomicdata on 2026-10-21.
Show all practicesHide 2 practices
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| 2021-03-31 | data.frame | 498 × 16 | No other package |
| 2021-04-02 | data.frame | 18 × 16 | No other package |
| 2021-10-14 | data.frame | 174 × 16 | No other package |
| 2022-04-13 | data.frame | 24 × 16 | No other package |
| 2022-10-19 | data.frame | 18 × 16 | No other package |
| metadata | data.frame | 732 × 16 | No other package |
| sampleMetadata | data.frame | 22,588 × 141 | No other package |
4 internal objects are bundled for the package's own use and not listed here.
Topics
Suggested by (6)
People
- Lucas schiffer author maintainer
- Sean Davis contributor
- Kelly Eckenrode contributor
- Samuel Gamboa-Tuz contributor
- Yoon-Ji Jung contributor
- Paolo Manghi contributor
- Chloe Mirzayi contributor
- Valerie Obenchain contributor
- Sehyun Oh contributor
- Edoardo Pasolli contributor
- Marcel Ramos contributor
- Audrey Renson contributor
- Nicola Segata contributor
- Levi Waldron author
- Jennifer Wokaty contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("curatedMetagenomicData")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nmeth.4468.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.