katdetectr
Bioc currentDetection, Characterization and Visualization of Kataegis in Sequencing Data
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
54 4 exported
Complexity
1.8 avg / 6 max
Call network
54 nodes / 52 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
2,674
Files
55
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
50
Testing
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
92.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 10includes a package overview page
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 10% with a bibliography file
- Overview_katdetectr HTML
Repository practices
Checks run against github.com/erasmusmc-ccbc/katdetectr on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
Topics
People
- Daan Hazelaar author maintainer
- Job van Riet author
- Harmen van de Werken thesis advisor
Cite
Cite this package
Run in R for the authors' entry:
citation("katdetectr")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/gigascience/giad081.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.