DOI: 10.18129/B9.bioc.RareVariantVis    

This package is for version 3.10 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: 3.10

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")):


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PDF R Script RareVariantVis
PDF   Reference Manual


biocViews GenomicVariation, Sequencing, Software, WholeGenome
Version 2.14.0
In Bioconductor since BioC 3.2 (R-3.2) (4.5 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
Suggests knitr
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package RareVariantVis_2.14.0.tar.gz
Windows Binary RareVariantVis_2.14.0.zip
Mac OS X 10.11 (El Capitan) RareVariantVis_2.14.0.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/
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