R Observatory: Metrics for ChAMP version 2.42.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ChAMP

Bioc current

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

v2.42.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.13 · Oct 15, 2013

Current · Requires R 4.6

1.0 In 26 of 49 releases 3.23

Description

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

29 20 exported

Complexity

13.8 avg / 41 max

Call network

29 nodes / 20 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.

Code

Structure

Lines of code

7,580

Files

108

Compiled share

0%

Has compiled src

No

Language breakdown

R 4,709 (62.1%)Docs 1,263 (16.7%)Vignettes 1,608 (21.2%)

API

Exported functions

20

Internal functions

4

Recent export changes

v3.8+1 champ.ebGSEA −1 champ.ebayGSEA

v3.7+1 champ.ebayGSEA

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

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

5.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.3

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

26

First release

2014-02-06

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

36

LOC over versions

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

Documentation

READMEYes · 73 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 98%
Return-value docs: 90%
References docs: 48%

Topics

Software › Technology › Microarray

Software › Technology › Microarray › MethylationArray

Software › WorkflowStep › Normalization

Software › Technology › Microarray › TwoChannel

CopyNumber

Software › AssayDomain › DNAMethylation

Depended on by (1)

Bioconductor (1)

GeoTcgaData

People

Tian Yuan maintainer author
Ankur Chakravarthy contributor
Andrew Feber contributor
Tiffany Morris contributor
Lee Stirling contributor
Andrew Teschendorff contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ChAMP")

Format

Yuan, T., Chakravarthy, A., Feber, A., Morris, T., Stirling, L., & Teschendorff, A. (2026). ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC (Version 2.42.0) [Computer software]. https://bioconductor.org/packages/ChAMP

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 ChAMP version 2.42.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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