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TVTB

TVTB: The VCF Tool Box


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TVTB")

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

Documentation

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

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

Details

biocViews Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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)
System Requirements
URL https://github.com/kevinrue/TVTB
Bug Reports https://github.com/kevinrue/TVTB/issues
See More
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
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Package Archives

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

Source Package TVTB_1.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) TVTB_1.28.0.tgz
macOS Binary (arm64) TVTB_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TVTB
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TVTB
Bioc Package Browser https://code.bioconductor.org/browse/TVTB/
Package Short Url https://bioconductor.org/packages/TVTB/
Package Downloads Report Download Stats