RareVariantVis
A suite for analysis of rare genomic variants in whole genome sequencing data
Bioconductor version: 3.24 · Package version: 2.41.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RareVariantVis")Details
| Maintainer | Tomasz Stokowy <tomasz.stokowy@k2.uib.no> |
| Author | Adam Gudys and Tomasz Stokowy |
| License | Artistic-2.0 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GenomicVariation, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/RareVariantVis/ |
Citation
From within R, enter citation("RareVariantVis"):
Adam Gudys and Tomasz Stokowy. RareVariantVis: A suite for analysis of rare genomic variants in whole genome sequencing data. doi:10.18129/B9.bioc.RareVariantVis, R package version 2.41.0, https://bioconductor.org/packages/RareVariantVis.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RareVariantVis_2.41.0.tar.gz |
| Windows binary (x86_64) | RareVariantVis_2.41.0.zip |
| macOS binary (arm64) | RareVariantVis_2.41.0.tgz |
| macOS binary (x86_64) | RareVariantVis_2.41.0.tgz |
Dependencies
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