R Observatory: Metrics for methrix version 1.26.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

methrix

Bioc current

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

v1.26.0 · Package record · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.10 · Oct 30, 2019

Current · Requires R 4.6

1.0 In 14 of 49 releases 3.23

Description

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

43 27 exported

Complexity

8.4 avg / 28 max

Call network

43 nodes / 44 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

4,843

Files

72

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,184 (65.7%)Tests 291 (6%)Docs 1,076 (22.2%)Vignettes 292 (6%)

API

Exported functions

27

Internal functions

16

Testing

Has tests

Yes

Test-to-code ratio

0.09

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

3

Dep constraint coverage

5.9%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.6

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

14

First release

2020-01-08

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

5

LOC over versions

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

Documentation

In the Bioconductor 3.23 release

READMEYes · 365 wordsVignettesYes · 1 · dynamicNEWSYes · 0% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 29
Examples that run: 85%23 run in a plain check · 4 never run
Exported functions with examples: 96%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 3%

Vignettes (1)

Methrix tutorial HTML

How these are measured

Repository practices

Upstream repositoryBeta

Checks run against github.com/compepigen/methrix on 2026-10-18.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Datasets

Bundled datasets · 1

Name	Class	Size	Also in
methrix_data	–	–	–

All of methrix's data objects

Topics

Software › AssayDomain › DNAMethylation

Software › Technology › Sequencing

Software › BiologicalQuestion › Coverage

Maintainer: Anand Mayakonda

Available on

CRANr2uBioconductorautoCRANCOPR

Suggested by (1)

methFuse

People

Anand Mayakonda author maintainer
Rajbir Batra contributor
Clarissa Feuerstein-Akgöz contributor
Joschka Hey contributor
Pavlo Lutsik contributor
Maximilian Schönung contributor
Reka Toth author

Cite

Cite this package

Run in R for the authors' entry:

citation("methrix")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btaa1048.

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 methrix version 1.26.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →