Skip to content
The VCF Tool Box
R Shell
Branch: master
Clone or download
Latest commit f80c02c Feb 20, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R oops Feb 20, 2019
inst oops Feb 20, 2019
man New argument zero.rm in method plotInfo to hide data points with valu… Nov 18, 2016
tests subsetting by [i,j] does not throw an error: intended Feb 24, 2018
vignettes removed mentions of biocLite Jul 20, 2018
.BBSoptions
.Rbuildignore
.gitignore Version 1.1.6. New plotInfo method; ADH1B gene example added. Nov 10, 2016
.travis.yml update Travis YAML from iSEE Jan 15, 2019
DESCRIPTION oops Feb 20, 2019
NAMESPACE The path() generic has moved from Rsamtools to BiocGenerics. Import it Dec 20, 2017
README.md removed mentions of biocLite Jul 20, 2018
TVTB.Rproj fix Shiny app: import variants from multiple VCF files May 30, 2017
appveyor.yml
codecov.yml

README.md

The VCF Tool Box (TVTB)

Software status

Platforms OS R CMD check Coverage1
AppVeyor2 Windows AppVeyor Build status N/A
Travis CI2 Linux Travis-CI Build Status Coverage Status
Bioc (devel) Multiple BioC-devel Build Status NA
Bioc (release) Multiple BioC-release Build Status NA

1Latest successful build; 2Bleeding edge original GitHub repository.

Description

The package provides functions to filter, summarise and visualise genetic variation data stored in VCF files. Functionalities are also demonstrated in a Shiny web-application.

Motivation

The VCF file format encodes a plethora of useful information, including optional predictions using the Ensembl Variant Effect Predictor (VEP) that can be parsed using expert packages such as VariantAnnotation and formatted into VCF objects. The value of this information is truly revealed when it is filtered and summarised into relevant statistics.

This package offers methods:

  • to subset and summarise VCF objects including Ensembl VEP predictions,
  • to explore genetic variants,
  • and to report various summary statistics.

Installation

Instructions to install the latest release of TVTB are available at: http://bioconductor.org/packages/release/bioc/html/TVTB.html

Using devtools, versions more recent than the official releases can be obtained:

install.packages("devtools")

The latest version pushed to Bioconductor release (may be more recent than the official release in the absence of version bump) :

devtools::install_github("Bioconductor-mirror/TVTB", ref="release-3.4")

The latest version pushed to Bioconductor devel (as above):

devtools::install_github("Bioconductor-mirror/TVTB", ref="master")

Original GitHub development repository:

devtools::install_github("kevinrue/TVTB")

Specific commit:

devtools::install_github("kevinrue/TVTB", ref="99966dda")

Graphical User Interface

Although nothing offers more flexibility than the command line interface, a Shiny web-application, the Shiny Variant Explorer (tSVE), offers a GUI to get familiar with the major functionalities of the package.

Tests

Unit tests and coverage implemented using the testthat package (CRAN).

Coverage excludes files:

  • AllClasses.R (Not executed at runtime)
  • tSVE.R (Requires interactive session)

License

Artistic License 2.0

You can’t perform that action at this time.