{ "_id": "6a1af8331d7bb097a09fabe8", "Package": "RareVariantVis", "Type": "Package", "Title": "A suite for analysis of rare genomic variants in whole genome\nsequencing data", "Version": "2.41.0", "Date": "2018-04-15", "Author": "Adam Gudys and Tomasz Stokowy", "Maintainer": "Tomasz Stokowy ", "Description": "Second version of RareVariantVis package aims to provide\ncomprehensive information about rare variants for your genome\ndata. It annotates, filters and presents genomic variants\n(especially rare ones) in a global, per chromosome way. For\ndiscovered rare variants CRISPR guide RNAs are designed, so the\nuser can plan further functional studies. Large structural\nvariants, including copy number variants are also supported.\nPackage accepts variants directly from variant caller - for\nexample GATK or Speedseq. Output of package are lists of\nvariants together with adequate visualization. Visualization of\nvariants is performed in two ways - standard that outputs png\nfigures and interactive that uses JavaScript d3 package.\nInteractive visualization allows to analyze trio/family data,\nfor example in search for causative variants in rare Mendelian\ndiseases, in point-and-click interface. The package includes\nhomozygous region caller and allows to analyse whole human\ngenomes in less than 30 minutes on a desktop computer.\nRareVariantVis disclosed novel causes of several rare monogenic\ndisorders, including one with non-coding causative variant -\nkeratolythic winter erythema.", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "GenomicVariation, Sequencing, WholeGenome", "NeedsCompilation": "no", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:24 UTC", "RemoteUrl": "https://github.com/bioc/RareVariantVis", "RemoteRef": "HEAD", "RemoteSha": "36b9f7600ec78500fe18bb985492edd3ca5fba6e", "Packaged": { "Date": "2026-05-30 09:47:21 UTC", "User": "root" }, "MD5sum": "a371bf58dde07abb37023efd7d69efbc", "_user": "bioc", "_type": "src", "_file": "RareVariantVis_2.41.0.tar.gz", "_fileid": 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"tomasz.stokowy@k2.uib.no", "login": "tstokowy", "description": "", "uuid": 16382685 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "BiocGenerics", "role": "Depends" }, { "package": "VariantAnnotation", "role": "Depends" }, { "package": "googleVis", "role": "Depends" }, { "package": "GenomicFeatures", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Imports" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Imports" }, { "package": "phastCons100way.UCSC.hg19", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "GenomicScores", "role": "Imports" }, { "package": "knitr", "role": "Suggests" } ], "_owner": 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"rareVariantVis" ], "_help": [ { "page": "callHomozygous", "title": "Call homozygous regions from sequencing data", "topics": [ "callHomozygous" ] }, { "page": "chromosomeVis", "title": "Visualization of all genomic variants on the chromosome", "topics": [ "chromosomeVis" ] }, { "page": "getCrisprGuides", "title": "Retrieve CRISPR/Cas9 guides.", "topics": [ "getCrisprGuides" ] }, { "page": "movingAverage", "title": "Computation of moving average", "topics": [ "movingAverage" ] }, { "page": "multipleVis", "title": "Interactive visualization of rare variants on the chromosome, applicable for multiple files", "topics": [ "multipleVis" ] }, { "page": "rareVariantVis", "title": "Interactive visualization of rare variants on the chromosome", "topics": [ "rareVariantVis" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocParallel", "BiocVersion", "Biostrings", 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