metabinR
Bioc currentAbundance and Compositional Based Binning of Metagenomes
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution. Inputs may be file paths or Biostrings/ShortRead sequence objects; results are returned as a MetabinResult S4 object wrapping cluster assignments, algorithm parameters, and input metadata.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
11 4 exported
Complexity
3.1 avg / 9 max
Call network
11 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
1,396
Files
80
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
6
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
4.4
System requirements
1
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
8
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
- 100%
- References docs
- 38%
Topics
People
- Anestis Gkanogiannis author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("metabinR")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.