To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.


DOI: 10.18129/B9.bioc.TVTB    

TVTB: The VCF Tool Box

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported


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 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License Artistic-2.0
Depends R (>= 3.4), methods, utils, stats
Imports AnnotationFilter, BiocGenerics(>= 0.19.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges(>= 2.7.1), reshape2, Rsamtools, S4Vectors(>= 0.11.11), SummarizedExperiment, VariantAnnotation(>= 1.19.9)
Suggests EnsDb.Hsapiens.v75(>= 0.99.7), shiny (>=, DT (>= 0.1.67), rtracklayer, BiocStyle(>= 2.1.23), knitr (>= 1.12), rmarkdown, testthat, covr, pander
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package TVTB_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) TVTB_1.2.0.tgz
Source Repository 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: