RnBeads
Bioc currentRnBeads
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
609 208 exported
Complexity
9.1 avg / 122 max
Call network
609 nodes / 1985 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
60,993
Files
439
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
209
Internal functions
400
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
4
Dep constraint coverage
10.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-04-16
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 297includes a package overview page
- Examples that run
- 1%1 run in a plain check · 152 only when donttest examples are enabled (R CMD check --as-cran) · 1 hold no code
- Exported functions with examples
- 58%
- Documented parameters
- 98%
- Return-value docs
- 98%
- Help pages citing references
- 2%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| epic_v1_manifest | data.frame | 142,137 × 5 | No other package |
| epic_v2_manifest | data.frame | 126,967 × 8 | No other package |
| interspecies_probes_v1 | vector | 15 elements | No other package |
| interspecies_probes_v2 | vector | 15 elements | No other package |
| lump.hg19 | list | 4 elements | No other package |
| lump.hg38 | list | 1 element | No other package |
| option_desc | data.frame | 111 × 3 | No other package |
| options | data.frame | 130 × 6 | No other package |
| predefined_predictor_27K | data.frame | 367 × 2 | No other package |
| predefined_predictor_450K | data.frame | 762 × 2 | No other package |
| predefined_predictor_Biseq_hg19 | data.frame | 157 × 2 | No other package |
| predefined_predictor_Biseq_hg38 | data.frame | 125 × 2 | No other package |
| predefined_predictor_RRBS_hg19 | data.frame | 157 × 2 | No other package |
| predefined_predictor_RRBS_hg38 | data.frame | 125 × 2 | No other package |
| remc_metadata_2013 | – | – | – |
| reportDescriptions | data.frame | 7 × 3 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (5)
People
- Fabian Mueller author maintainer
- Yassen Assenov author
- Christoph Bock author
- Pavlo Lutsik author
- Michael Scherer author
Cite
Cite this package
Run in R for the authors' entry:
citation("RnBeads")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-019-1664-9, 10.1038/nmeth.3115.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.