To install this package, start R and enter:

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

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

VariantTools

DOI: 10.18129/B9.bioc.VariantTools    

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

Tools for Exploratory Analysis of Variant Calls

Bioconductor version: Development (3.6)

Explore, diagnose, and compare variant calls using filters.

Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman

Maintainer: Michael Lawrence <michafla at gene.com>

Citation (from within R, enter citation("VariantTools")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantTools")

 

PDF R Script Introduction to VariantTools
PDF tutorial.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneticVariability, Genetics, Sequencing, Software
Version 1.19.1
In Bioconductor since BioC 2.11 (R-2.15) (5 years)
License Artistic-2.0
Depends S4Vectors(>= 0.9.25), IRanges(>= 1.99.2), GenomicRanges(>= 1.17.7), VariantAnnotation(>= 1.11.16), methods
Imports Rsamtools(>= 1.17.6), BiocGenerics, Biostrings, parallel, GenomicFeatures(>= 1.17.13), Matrix, rtracklayer(>= 1.25.3), BiocParallel, GenomeInfoDb, BSgenome, Biobase
LinkingTo
Suggests RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.13.4)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me HTSeqGenie
Suggests Me VariantToolsData
Build Report  

Package Archives

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

Package Source VariantTools_1.19.1.tar.gz
Windows Binary VariantTools_1.19.1.zip
Mac OS X 10.11 (El Capitan) VariantTools_1.19.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/VariantTools
Package Short Url http://bioconductor.org/packages/VariantTools/
Package Downloads Report Download Stats

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