VariantTools
Bioc currentTools for Exploratory Analysis of Variant Calls
Release Lineage
Entered 2.11 · Oct 3, 2012
Current · Requires R 4.6
Description
Explore, diagnose, and compare variant calls using filters.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
77 22 exported
Complexity
2 avg / 12 max
Call network
77 nodes / 54 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
2,887
Files
111
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
52
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
96.2%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
43.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
28
First release
2012-10-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15
- Examples that run
- 92%11 run in a plain check (1 of them under a condition) · 1 never run
- Exported functions with examples
- 79%
- Documented parameters
- 94%
- Return-value docs
- 100%
- Help pages citing references
- 7%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| coverage_H1993 | – | – | – |
| coverage_H2073 | – | – | – |
| genome_p53 | – | – | – |
| p53 | – | – | – |
| tallies_H1993 | – | – | – |
| tallies_H2073 | – | – | – |
Topics
Depended on by (4)
Bioconductor (4)
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("VariantTools")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.