Package: TVTB
Type: Package
Title: TVTB: The VCF Tool Box
Version: 1.39.0
Date: 2025-08-05
Authors@R: person("Kevin", "Rue-Albrecht", role = c("aut", "cre"),
    email = "kevinrue67@gmail.com")
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).
License: Artistic-2.0
Depends: R (>= 3.4), methods, utils, stats
Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
        Biostrings, ensembldb, Seqinfo, 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 (>= 0.13.2.9005), DT
        (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>=
        1.12), rmarkdown, testthat, covr, pander
biocViews: Software, Genetics, GeneticVariability, GenomicVariation,
        DataRepresentation, GUI, Genetics, DNASeq, WholeGenome,
        Visualization, MultipleComparison, DataImport,
        VariantAnnotation, Sequencing, Coverage, Alignment,
        SequenceMatching
Collate: utils.R tSVE.R AllClasses.R AllGenerics.R Genotypes-class.R
        TVTBparam-class.R VcfFilterRules-class.R parseCSQToGRanges.R
        countGenos-methods.R autodetectGenotypes.R
        addCountGenos-methods.R addFrequencies-methods.R
        addOverallFrequencies-methods.R
        addPhenoLevelFrequencies-methods.R dropInfo.R readVcf-methods.R
        variantsInSamples-methods.R vepInPhenoLevel-methods.R
        plotInfo.R pairsInfo.R show-methods.R
VignetteBuilder: knitr
URL: https://github.com/kevinrue/TVTB
BugReports: https://github.com/kevinrue/TVTB/issues
Config/Bioconductor/UnsupportedPlatforms: windows
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:44:36 UTC
RemoteUrl: https://github.com/bioc/TVTB
RemoteRef: HEAD
RemoteSha: c77deb7c910e894acf8844311da6fcca42390faf
NeedsCompilation: no
Packaged: 2026-07-06 06:42:48 UTC; root
Author: Kevin Rue-Albrecht [aut, cre]
Maintainer: Kevin Rue-Albrecht <kevinrue67@gmail.com>