QDNAseq
Bioc currentQuantitative DNA Sequencing for Chromosomal Aberrations
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
25 9 exported
Complexity
5.4 avg / 32 max
Call network
25 nodes / 25 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
6,935
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
28
Internal functions
16
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
89.3%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
82.6%
Unsafe pattern score
0
Dep constraint coverage
62.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.1.0
System requirements
–
C++ standard
–
License
GPL
License flags
not SPDX, not OSI
History
Versions
25
First release
2014-06-13
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27includes a package overview page
- Examples that run
- 81%17 run in a plain check · 4 never run
- Exported functions with examples
- 100%
- Documented parameters
- 90%
- Return-value docs
- 76%
- Help pages citing references
- 4%
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/ccagc/qdnaseq on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
Topics
Depended on by (6)
Bioconductor (6)
People
- Daoud Sie author maintainer
- Henrik Bengtsson author
- Ilari Scheinin author
- Erik van Dijk contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("QDNAseq")The package provides a citation file, so citation() returns the authors' own entry.
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.