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.
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
3,696
Files
55
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
0
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.49
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
4.1.0
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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (5)
Bioconductor (5)
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