recountmethylation
Bioc currentAccess and analyze public DNA methylation array data compilations
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
44 21 exported
Complexity
4.8 avg / 17 max
Call network
44 nodes / 35 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,983
Files
90
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
21
Internal functions
23
Testing & CI
Has tests
Yes
Test-to-code ratio
0.01
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
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
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
- Examples that run
- 95%
- Documented parameters
- 99%
- Return-value docs
- 100%
- References docs
- 14%
Topics
People
- Sean K Maden maintainer author
- Kyle Ellrott author
- Kasper D Hansen author
- Abhinav Nellore author
- Reid F Thompson author
- Brian Walsh author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("recountmethylation")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.
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.