Package: RareVariantVis
Type: Package
Title: A suite for analysis of rare genomic variants in whole genome
        sequencing data
Version: 2.2.0
Date: 2017-02-21
Author: Adam Gudys and Tomasz Stokowy
Maintainer: Tomasz Stokowy <tomasz.stokowy@k2.uib.no>
Description: 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. 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.
License: Artistic-2.0
LazyData: TRUE
Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures
Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools,
        BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
        phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores
Suggests: knitr
VignetteBuilder: knitr
biocViews: GenomicVariation, Sequencing, WholeGenome
NeedsCompilation: no
Packaged: 2017-04-25 01:04:52 UTC; biocbuild
Built: R 3.4.0; ; 2017-04-25 06:34:09 UTC; windows
