microbiome
Bioc currentMicrobiome Analytics
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
Utilities for microbiome analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
126 77 exported
Complexity
5.5 avg / 41 max
Call network
126 nodes / 167 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
13,316
Files
210
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
77
Internal functions
49
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
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
3.6.0
System requirements
–
C++ standard
–
License
BSD_2_clause + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2018-02-22
Latest release
2026-04-28
Avg cadence
182 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
- Help pages
- 90 (5 internal)includes a package overview page
- Examples that run
- 83%70 run in a plain check · 1 never run · 13 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 63%
- microbiome R package HTML
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/microbiome/microbiome on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| atlas1006 | – | – | – |
| dietswap | – | – | – |
| hitchip.taxonomy | list | 2 elements | No other package |
| peerj32 | list | 4 elements | No other package |
Topics
Depended on by (4)
Bioconductor (2)
CRAN (2)
Suggested by (7)
People
- Leo Lahti author maintainer
- Sudarshan Shetty author
Cite
Cite this package
Run in R for the authors' entry:
citation("microbiome")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.