To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("RareVariantVis")
In most cases, you don't need to download the package archive at all.
Bioconductor version: Release (3.5)
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.
Author: Adam Gudys and Tomasz Stokowy
Maintainer: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>
Citation (from within R,
enter citation("RareVariantVis")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("RareVariantVis")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RareVariantVis")
R Script | RareVariantVis | |
Reference Manual |
biocViews | GenomicVariation, Sequencing, Software, WholeGenome |
Version | 2.2.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (2 years) |
License | Artistic-2.0 |
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 |
LinkingTo | |
Suggests | knitr |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | RareVariantVis_2.2.0.tar.gz |
Windows Binary | RareVariantVis_2.2.0.zip |
Mac OS X 10.11 (El Capitan) | RareVariantVis_2.2.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/RareVariantVis |
Package Short Url | http://bioconductor.org/packages/RareVariantVis/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: