RareVariantVis
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RareVariantVis.
A suite for analysis of rare genomic variants in whole genome sequencing data
Bioconductor version: 3.9
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.
Author: Adam Gudys and Tomasz Stokowy
Maintainer: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>
citation("RareVariantVis")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RareVariantVis")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RareVariantVis")| RareVariantVis | R Script | |
| Reference Manual |
Details
| biocViews | GenomicVariation, Sequencing, Software, WholeGenome |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RareVariantVis_2.12.0.tar.gz |
| Windows Binary | RareVariantVis_2.12.0.zip |
| Mac OS X 10.11 (El Capitan) | RareVariantVis_2.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RareVariantVis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RareVariantVis |
| Bioc Package Browser | https://code.bioconductor.org/browse/RareVariantVis/ |
| Package Short Url | https://bioconductor.org/packages/RareVariantVis/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |