metagenomeSeq
Bioc currentStatistical analysis for sparse high-throughput sequencing
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
83 63 exported
Complexity
3.7 avg / 14 max
Call network
83 nodes / 88 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
8,833
Files
165
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
63
Internal functions
11
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
CI present
Yes
CI type
["travis"]
PR gated
No
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
3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
27
First release
2013-07-25
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
13
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
- 98%
- References docs
- 3%
Topics
Depended on by (16)
Bioconductor (14)
CRAN (2)
People
Joseph N. Paulson
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("metagenomeSeq")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.