DAMEfinder
Bioc currentFinds DAMEs - Differential Allelicly MEthylated regions
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
'DAMEfinder' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 11 exported
Complexity
8.4 avg / 23 max
Call network
19 nodes / 12 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
4,518
Files
75
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
8
Testing
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-10-07
Latest release
2026-04-28
Avg cadence
182 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
- 22 (4 internal)includes a package overview page
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- DAMEfinder Workflow HTML
Repository practices
Checks run against github.com/markrobinsonuzh/damefinder on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| CRC1_chr19.qs.CG.2 | data.frame | 5,334 × 8 | No other package |
| NORM1_chr19.qs.CG.2 | data.frame | 5,317 × 8 | No other package |
| extractbams_output | list | 8 elements | No other package |
| readtuples_output | list | 5 elements | No other package |
Topics
People
- Stephany Orjuela author maintainer
- Dania Machlab author
- Mark Robinson author
Cite
Cite this package
Run in R for the authors' entry:
citation("DAMEfinder")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13072-020-00346-8.
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.