To install this package, start R and enter:

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

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

RareVariantVis

   

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see RareVariantVis.

Visualization of rare variants in whole genome sequencing data

Bioconductor version: 3.3

Genomic variants can be analyzed and visualized using many tools. Unfortunately, number of tools for global interrogation of variants is limited. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases.

Author: Tomasz Stokowy

Maintainer: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("RareVariantVis")

 

PDF R Script RareVariantVis
PDF   Reference Manual

Details

biocViews GenomicVariation, Sequencing, Software, WholeGenome
Version 1.6.2
In Bioconductor since BioC 3.2 (R-3.2) (1 year)
License Artistic-2.0
Depends BiocGenerics, VariantAnnotation, googleVis
Imports S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
LinkingTo
Suggests knitr, AshkenazimSonChr21
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source RareVariantVis_1.6.2.tar.gz
Windows Binary RareVariantVis_1.6.2.zip
Mac OS X 10.9 (Mavericks) RareVariantVis_1.6.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RareVariantVis/tree/release-3.3
Package Short Url http://bioconductor.org/packages/RareVariantVis/
Package Downloads Report Download Stats

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