TVTB

DOI: 10.18129/B9.bioc.TVTB    

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

TVTB: The VCF Tool Box

Bioconductor version: Development (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TVTB", version = "3.9")

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
PDF 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 1.9.0
In Bioconductor since BioC 3.4 (R-3.3) (2 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(>= 2.7.1), reshape2, Rsamtools, S4Vectors(>= 0.11.11), 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_1.9.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) TVTB_1.9.0.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 http://bioconductor.org/packages/TVTB/
Package Downloads Report Download Stats

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