SeqVarTools
Bioc currentTools for variant data
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
74 7 exported
Complexity
1.9 avg / 7 max
Call network
74 nodes / 39 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
5,450
Files
84
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
66
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
26
First release
2013-10-14
Latest release
2026-07-09
Avg cadence
185 days
Cold removal rate
–
Dep drift
20
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 28includes a package overview page
- Examples that run
- 96%25 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 0%
- Help pages citing references
- 11%
Repository practices
Checks run against github.com/smgogarten/seqvartools on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| hapmap_annotation | data.frame | 22 × 6 | No other package |
| hapmap_annotation_DD | data.frame | 6 × 2 | No other package |
| pedigree | data.frame | 90 × 6 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SeqVarTools")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.