Maaslin2
Bioc current"Multivariable Association Discovery in Population-scale Meta-omics Studies"
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 1 exported
Complexity
9.5 avg / 70 max
Call network
16 nodes / 12 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
3,227
Files
19
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
11
Testing
Has tests
Yes
Test-to-code ratio
0.17
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
System requirements
–
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
182 days
Cold removal rate
–
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
- 1
- Examples that run
- 100%1 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Maaslin2 HTML
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/biobakery/maaslin2 on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| HMP2_metadata | data.frame | 1,595 × 12 | No other package |
| HMP2_taxonomy | data.frame | 1,595 × 88 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (2)
People
- Sagun Maharjan author maintainer
- Thomas Kuntz author
- Himel Mallick author
- Ali Rahnavard author
Cite
Cite this package
Run in R for the authors' entry:
citation("Maaslin2")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pcbi.1009442.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.