MMUPHin
Bioc currentMeta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
53 4 exported
Complexity
3.9 avg / 21 max
Call network
53 nodes / 65 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
5,121
Files
85
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
47
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
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
System requirements
1 externalglpk (>= 4.57)
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
179 days
Cold removal rate
100%
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 52 (44 internal)
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 8%
- MMUPHin HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| CRC_abd | matrix | 484 × 551 | No other package |
| CRC_meta | data.frame | 551 × 28 | No other package |
| vaginal_abd | matrix | 119 × 86 | No other package |
| vaginal_meta | data.frame | 86 × 24 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MMUPHin")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.