dmrseq
Bioc currentDetection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 6 exported
Complexity
14.5 avg / 107 max
Call network
31 nodes / 33 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
4,831
Files
34
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
25
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
4.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
17
First release
2018-08-07
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 10
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 10%
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 |
|---|---|---|---|
| BS.chr21 | – | – | – |
| annot.chr21 | – | – | – |
| dmrs.ex | – | – | – |
Topics
Depended on by (2)
Bioconductor (2)
People
- Keegan Korthauer maintainer author
- Yuval Benjamini author
- Sutirtha Chakraborty author
- Rafael Irizarry author
Cite
Cite this package
Run in R for the authors' entry:
citation("dmrseq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/biostatistics/kxy007.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.