Damsel
Bioc currentDamsel: an end to end analysis of DamID
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
54 21 exported
Complexity
2.9 avg / 15 max
Call network
54 nodes / 45 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
4,061
Files
79
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
22
Internal functions
33
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
3
Docs
Roxygen coverage
95.5%
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
4.4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-08-28
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (2 internal)includes a package overview page
- Examples that run
- 100%22 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 46%
- Damsel-workflow HTML
Repository practices
Checks run against github.com/oshlack/damsel on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| dros_counts | data.frame | 80,000 × 11 | No other package |
Topics
People
- Caitlin Page author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Damsel")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 v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.