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RnBeads

Bioc current

RnBeads

v2.30.0 · software · GPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.1 · Apr 17, 2015

Current · Requires R 4.6

1.0 In 23 of 49 releases 3.23

Description

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

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 →
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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

60,993

Files

440

Compiled share

0%

Has compiled src

No

Language breakdown

R 46,443 (76.1%)Tests 1 (0%)Docs 12,038 (19.7%)Vignettes 2,511 (4.1%)

API

Exported functions

209

Internal functions

400

Recent export changes

v3.8+3 rnb.combine.seq, rnb.execute.sex.prediction, rnb.step.cnv  −1 rnb.execute.gender.prediction
v3.6+23 apply.iEVORA, diffVar, downloadLolaDbs +20 more  −2 performEnrichment.diffMeth, read.geo

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

No

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

v3.1: 46,098 LOCv3.2: 48,023 LOCv3.3: 49,103 LOCv3.4: 50,495 LOCv3.5: 50,398 LOCv3.6: 56,788 LOCv3.7: 56,816 LOCv3.8: 57,177 LOCv3.9: 57,468 LOCv3.10: 58,045 LOCv3.11: 58,050 LOCv3.12: 58,708 LOCv3.13: 59,432 LOCv3.14: 59,442 LOCv3.15: 59,442 LOCv3.16: 59,784 LOCv3.17: 59,791 LOCv3.18: 59,797 LOCv3.19: 60,664 LOCv3.20: 60,664 LOCv3.21: 60,666 LOCv3.22: 60,734 LOCv3.23: 60,993 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo
Examples that run
1%
Documented parameters
98%
Return-value docs
98%
References docs
2%

Topics

Software › AssayDomain › DNAMethylation
Software › Technology › Microarray › MethylationArray
Software › Technology › Sequencing › MethylSeq
Software › ResearchField › Epigenetics
Software › WorkflowStep › QualityControl
Software › WorkflowStep › Preprocessing
Software › WorkflowStep › BatchEffect
Software › BiologicalQuestion › DifferentialMethylation
Software › Technology › Sequencing
Software › AssayDomain › CpGIsland
Software › ResearchField › Immunology › ImmunoOncology
Software › Technology › Microarray › TwoChannel
Software › Infrastructure › DataImport

Depended on by (6)

Bioconductor (6)

MAGAR RnBeads.hg19 RnBeads.hg38 RnBeads.mm10 RnBeads.mm9 RnBeads.rn5

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