R Observatory: Metrics for ELMER version 2.35.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ELMER

Bioc current

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

v2.35.1 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.2 · Oct 14, 2015

Current · Requires R 4.6

1.0 In 22 of 49 releases 3.23

Description

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

74 38 exported

Complexity

7.6 avg / 48 max

Call network

74 nodes / 108 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

14,434

Files

153

Compiled share

0%

Has compiled src

No

Language breakdown

R 7,510 (52%)Tests 1,150 (8%)Docs 3,183 (22.1%)Vignettes 2,591 (18%)

API

Exported functions

38

Internal functions

36

Recent export changes

v3.8+4 createBigWigDNAmetArray, createIGVtrack, getRegionNearGenes +1 more

v3.7+5 calculateEnrichement, getRandomPairs, getTFtargets +2 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.15

testthat edition

–

CI present

Yes

CI type

["travis","appveyor"]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

6.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.4.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

22

First release

2016-04-25

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

41

LOC over versions

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

Documentation

READMEYes · 100 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 62%
Documented parameters: 97%
Return-value docs: 63%
References docs: 14%

Topics

Software › AssayDomain › DNAMethylation

Software › AssayDomain › GeneExpression

Software › BiologicalQuestion › MotifAnnotation

Software

Software › BiologicalQuestion › GeneRegulation

Software › AssayDomain › Transcription

Software › WorkflowStep › Visualization › Network

Depended on by (2)

Bioconductor (2)

TCGAWorkflow TCGAbiolinksGUI

People

Tiago Chedraoui Silva author maintainer
Benjamin Berman author
Simon Coetzee author
Peggy Farnham author
Nicole Gull contributor
Peter Laird contributor
Dechen Li contributor
Hui Shen contributor
Lijing Yao author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ELMER")

Format

Chedraoui Silva, T., Berman, B., Coetzee, S., Farnham, P., Gull, N., Laird, P., Li, D., Shen, H., & Yao, L. (2026). ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes (Version 2.35.1) [Computer software]. https://bioconductor.org/packages/ELMER

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ELMER version 2.35.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

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.

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