TVTB

This is the development version of TVTB; for the stable release version, see TVTB.

TVTB: The VCF Tool Box

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TVTB")

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

Documentation


Reference Manual	PDF

Details

biocViews	Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome
Version	1.27.0
In Bioconductor since	BioC 3.4 (R-3.3) (7 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)
Linking To
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
System Requirements
Enhances
URL	https://github.com/kevinrue/TVTB
Bug Reports	https://github.com/kevinrue/TVTB/issues

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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/TVTB
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TVTB
Package Short Url	https://bioconductor.org/packages/TVTB/
Package Downloads Report	Download Stats