phyloseq
Bioc currentHandling and analysis of high-throughput microbiome census data
Release Lineage
Entered 2.10 · Apr 2, 2012
Current · Requires R 4.6
Description
phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
155 109 exported
Complexity
3.6 avg / 49 max
Call network
155 nodes / 103 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
23,347
Files
217
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
140
Internal functions
46
Testing
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
9
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
29
First release
2012-09-12
Latest release
2026-04-28
Avg cadence
182 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
- 132 (20 internal)includes a package overview page
- Examples that run
- 73%81 run in a plain check · 30 hold no code
- Exported functions with examples
- 96%
- Documented parameters
- 99%
- Return-value docs
- 89%
- Help pages citing references
- 14%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/joey711/phyloseq on 2026-10-11.
GitHub Pages site last deployed 2020-02-14
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GP_otu_table_rand_short | data.frame | 499 × 30 | No other package |
| GlobalPatterns | – | – | – |
| enterotype | – | – | – |
| esophagus | – | – | – |
| gp500-uuf | data.frame | 27 × 28 | No other package |
| gp500-wuf | data.frame | 27 × 28 | No other package |
| gp500-wufu | data.frame | 27 × 28 | No other package |
| gp500test.env | data.frame | 3,092 × 3 | No other package |
| master_map | data.frame | 27 × 7 | No other package |
| rformat_dist_0.03 | data.frame | 14 × 5,277 | No other package |
| soilrep | – | – | – |
| study_gp | data.frame | 27 × 7 | No other package |
Topics
Depended on by (42)
Show 72 packagesHide 72 packages
Bioconductor (23)
CRAN (19)
Suggested by (32)
People
- Paul J. McMurdie author maintainer
- Scott Chamberlain contributor
- Susan Holmes author
- Gregory Jordan contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("phyloseq")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.