DESCRIPTION

Package: TVTB
Type: Package
Title: TVTB: The VCF Tool Box
Version: 1.31.2
Date: 2024-07-05
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,
    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 (>= 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