DOI: 10.18129/B9.bioc.TVTB    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TVTB.

TVTB: The VCF Tool Box

Bioconductor version: 3.12

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).

Author: Kevin Rue-Albrecht [aut, cre]

Maintainer: Kevin Rue-Albrecht <kevinrue67 at>

Citation (from within R, enter citation("TVTB")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Introduction to TVTB
HTML R Script The Shiny Variant Explorer
HTML R Script VCF filter rules
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome
Version 1.16.0
In Bioconductor since BioC 3.4 (R-3.3) (4.5 years)
License Artistic-2.0
Depends R (>= 3.4), methods, utils, stats
Imports AnnotationFilter, BiocGenerics(>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges(>= 2.21.6), reshape2, Rsamtools, S4Vectors(>= 0.25.14), SummarizedExperiment, VariantAnnotation(>= 1.19.9)
Suggests EnsDb.Hsapiens.v75(>= 0.99.7), shiny (>=, DT (>= 0.1.67), rtracklayer, BiocStyle(>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TVTB_1.16.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) TVTB_1.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: