EpiMix
Bioc currentEpiMix: an integrative tool for the population-level analysis of DNA methylation
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
103 20 exported
Complexity
6.1 avg / 51 max
Call network
103 nodes / 128 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
10,781
Files
117
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
83
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
8
Dep constraint coverage
2.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-04-03
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
- 85 (44 internal)
- Examples that run
- 19%4 run in a plain check · 17 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 95%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 1%
- vignette HTML
Repository practices
Checks run against github.com/gevaertlab/epimix on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Topics
Depended on by (1)
Bioconductor (1)
People
- Yuanning Zheng author maintainer
- Olivier Gevaert author
- John Jun author
- Markus Sujansky author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("EpiMix")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.