TVTB

DOI: 10.18129/B9.bioc.TVTB    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TVTB.

TVTB: The VCF Tool Box

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome
Version	1.16.0
In Bioconductor since	BioC 3.4 (R-3.3) (4.5 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)
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/kevinrue/TVTB
BugReports	https://github.com/kevinrue/TVTB/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TVTB_1.16.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	TVTB_1.16.0.tgz
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