MIRA
Bioc currentMethylation-Based Inference of Regulatory Activity
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 11 exported
Complexity
6.3 avg / 34 max
Call network
29 nodes / 32 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
3,907
Files
48
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
18
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
CI present
Yes
CI type
["travis"]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
18
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-11-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 94%
- Return-value docs
- 100%
- References docs
- 5%
Topics
Depended on by (1)
Bioconductor (1)
People
- John Lawson author maintainer
- Christoph Bock contributor
- Nathan Sheffield author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MIRA")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.