methylPipe
Bioc currentBase resolution DNA methylation data analysis
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
24 0 exported
Complexity
9.4 avg / 44 max
Call network
24 nodes / 9 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
3,273
Files
51
Compiled share
1.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
20
Internal functions
1
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
2
Dep constraint coverage
5.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2.0
System requirements
–
C++ standard
–
License
GPL(>=2)
License flags
not SPDX, not OSI
History
Versions
24
First release
2015-03-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23includes a package overview page
- Examples that run
- 85%17 run in a plain check · 3 hold no code
- Exported functions with examples
- 89%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 0%
- methylPipe.pdf PDF
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DMRs | – | – | – |
| GR_chr20 | – | – | – |
| H1_chr20_CG_10k | data.frame | 9,068 × 6 | No other package |
| H1_chr20_CG_10k_tabix_out | – | – | – |
| H1_chr20_CG_10k_tabix_out.txt.gz | – | – | – |
| IMR90_chr20_CG_10k_tabix_out | – | – | – |
| IMR90_chr20_CG_10k_tabix_out.txt.gz | – | – | – |
| gec.H1 | – | – | – |
| gec.IMR90 | – | – | – |
| uncov_GR | – | – | – |
Topics
Depended on by (2)
Bioconductor (2)
People
- Mattia Furlan contributor maintainer
- Kamal Kishore author
- Mattia Pelizzola author
Cite
Cite this package
Run in R for the authors' entry:
citation("methylPipe")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-015-0742-6.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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.