RareVariantVis

DOI: 10.18129/B9.bioc.RareVariantVis    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RareVariantVis.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RareVariantVis")

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("RareVariantVis")

 

PDF	R Script	RareVariantVis
PDF		Reference Manual

Details

biocViews	GenomicVariation, Sequencing, Software, WholeGenome
Version	2.12.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 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
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Build Report

Package Archives

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

Source Package	RareVariantVis_2.12.0.tar.gz
Windows Binary	RareVariantVis_2.12.0.zip
Mac OS X 10.11 (El Capitan)	RareVariantVis_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RareVariantVis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RareVariantVis
Package Short Url	https://bioconductor.org/packages/RareVariantVis/
Package Downloads Report	Download Stats