Package: RareVariantVis
Type: Package
Title: A suite for analysis of rare genomic variants in whole genome
        sequencing data
Version: 2.38.0
Date: 2018-04-15
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. 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.
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
VignetteBuilder: knitr
biocViews: GenomicVariation, Sequencing, WholeGenome
NeedsCompilation: no
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:26:20 UTC
RemoteUrl: https://github.com/bioc/RareVariantVis
RemoteRef: RELEASE_3_22
RemoteSha: 883a1657ae66410f83153fdf8587ade76411c4ef
Packaged: 2026-02-24 08:36:19 UTC; root
Built: R 4.5.2; ; 2026-02-24 08:40:16 UTC; windows
