DOI: 10.18129/B9.bioc.TVTB    

TVTB: The VCF Tool Box

Bioconductor version: Release (3.6)

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")):


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PDF R Script The Shiny Variant Explorer
HTML R Script Introduction to TVTB
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 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
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(>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander
Depends On Me
Imports Me
Suggests Me
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