To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TVTB")

In most cases, you don't need to download the package archive at all.

TVTB

 

   

TVTB: The VCF Tool Box

Bioconductor version: Release (3.4)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TVTB")

Documentation

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 1.0.2
In Bioconductor since BioC 3.4 (R-3.3) (< 6 months)
License Artistic-2.0
Depends R (>= 3.3), methods, utils, stats
Imports BiocGenerics(>= 0.19.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, ggplot2, 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(>= 2.1.23), knitr (>= 1.12), rmarkdown, testthat, covr
SystemRequirements
Enhances
URL https://github.com/kevinrue/TVTB
BugReports https://github.com/kevinrue/TVTB/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source TVTB_1.0.2.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks) TVTB_1.0.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TVTB/tree/release-3.4
Package Short Url http://bioconductor.org/packages/TVTB/
Package Downloads Report Download Stats

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