biomformat
Bioc currentAn interface package for the BIOM file format
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
This is an R package for interfacing with the BIOM file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 7 exported
Complexity
5.2 avg / 20 max
Call network
13 nodes / 4 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
3,945
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
6
Testing
Has tests
Yes
Test-to-code ratio
0.48
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
66.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-15
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22includes a package overview page
- Examples that run
- 100%21 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 93%
- Help pages citing references
- 27%
Repository practices
Checks run against github.com/joey711/biomformat on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Topics
Depended on by (3)
Bioconductor (3)
Suggested by (8)
People
- Paul J. McMurdie author maintainer
- Joseph N. Paulson author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("biomformat")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.