MotifPeeker

Bioc current

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

v1.4.0 · software · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.21 · Apr 16, 2025

Current · Requires R 4.6

1.0 In 3 of 49 releases 3.23

Description

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. Motif Discovery Enrichment Analysis) Statistics for the frequency of ab-initio discovered motifs enriched in the datasets and compared with known motifs.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

48 19 exported

Complexity

3.9 avg / 16 max

Call network

48 nodes / 47 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

7,265

Files

181

Compiled share

Has compiled src

Language breakdown

R 3,121 (43%)Tests 714 (9.8%)Docs 2,797 (38.5%)Vignettes 633 (8.7%)

API

Exported functions

Internal functions

Recent export changes

v3.23+2 bootstrap_distances, get_df_distances_bootstrapped

v3.21+18 %>%, MotifPeeker, calc_frip +15 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.23

testthat edition

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

95%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

Unsafe pattern score

Dep constraint coverage

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.6.0

System requirements

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

First release

2025-04-15

Latest release

2026-04-28

Avg cadence

189 days

Cold removal rate

–

Dep drift

LOC over versions

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

Documentation

READMEYes · 1,468 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › Epigenetics

Software › ResearchField › Genetics

Software › WorkflowStep › QualityControl

Software › Technology › Sequencing › ChIPSeq

Software › WorkflowStep › MultipleComparison

Software › ResearchField › FunctionalGenomics

Software › BiologicalQuestion › MotifDiscovery

Software › BiologicalQuestion › SequenceMatching

Software

Software › WorkflowStep › Alignment

People

Hiranyamaya Dash maintainer author
Thomas Roberts author
Nathan Skene author
Maria Weinert author

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