DNAfusion
Bioc currentIdentification of gene fusions using paired-end sequencing
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 8 exported
Complexity
7.2 avg / 12 max
Call network
10 nodes / 14 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
1,629
Files
26
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
2
Testing
Has tests
Yes
Test-to-code ratio
0.15
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
4.4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/ctriermaansson/dnafusion on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Topics
People
- Christoffer Trier Maansson author maintainer
- Emma Roger Andersen contributor reviewer
- Peter Meldgaard data contributor
- Boe Sandahl Sorensen reviewer funder
- Maiken Parm Ulhoi data contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("DNAfusion")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-023-05259-3.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.