To install this package, start R and enter:

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

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RareVariantVis

DOI: 10.18129/B9.bioc.RareVariantVis    

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

A suite for analysis of rare genomic variants in whole genome sequencing data

Bioconductor version: Development (3.6)

Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants 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, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.

Author: Adam Gudys and 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 2.4.0
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License Artistic-2.0
Depends BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures
Imports S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores
LinkingTo
Suggests knitr
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.

Source Package RareVariantVis_2.4.0.tar.gz
Windows Binary RareVariantVis_2.4.0.zip
Mac OS X 10.11 (El Capitan) RareVariantVis_2.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RareVariantVis
Package Short Url http://bioconductor.org/packages/RareVariantVis/
Package Downloads Report Download Stats

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