ANCOMBC
Bioc currentMicrobiome differential abudance and correlation analyses with bias correction
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
34 7 exported
Complexity
7.8 avg / 46 max
Call network
34 nodes / 39 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
9,441
Files
41
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
27
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.02
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
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2021-03-09
Latest release
2026-04-28
Avg cadence
159 days
Cold removal rate
–
Dep drift
42
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 63% with a bibliography file
Repository practices
Checks run against github.com/frederickhuanglin/ancombc on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| QMP | matrix | 106 × 91 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (3)
People
- Huang Lin maintainer author
Cite
Cite this package
Run in R for the authors' entry:
citation("ANCOMBC")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 v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.