TVTB

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TVTB.

TVTB: The VCF Tool Box

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome

Version 1.20.0

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

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

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package TVTB_1.20.0.tar.gz

Windows Binary

macOS 10.13 (High Sierra) TVTB_1.20.0.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

Old Source Packages for BioC 3.14 Source Archive