TVTB
Bioc currentTVTB: The VCF Tool Box
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 7 exported
Complexity
2.7 avg / 10 max
Call network
36 nodes / 26 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
7,943
Files
108
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
29
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.67
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
20%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-23
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 19includes a package overview page
- Examples that run
- 100%18 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 67%
- Help pages citing references
- 11%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/kevinrue/tvtb on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| integrated_samples | data.frame | 2,504 × 4 | No other package |
| moderate_pheno | data.frame | 176 × 4 | No other package |
Topics
People
- Kevin Rue-Albrecht author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("TVTB")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.