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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.
RareVariantVis
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see RareVariantVis.
Visualization of rare variants in whole genome sequencing data
Bioconductor version: 3.3
Genomic variants can be analyzed and visualized using many tools. Unfortunately, number of tools for global interrogation of variants is limited. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization 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.
Author: Tomasz Stokowy
Maintainer: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>
Citation (from within R,
enter citation("RareVariantVis")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RareVariantVis")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RareVariantVis")
| R Script | RareVariantVis | |
| Reference Manual |
Details
| biocViews | GenomicVariation, Sequencing, Software, WholeGenome |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1 year) |
| License | Artistic-2.0 |
| Depends | BiocGenerics, VariantAnnotation, googleVis |
| Imports | S4Vectors, IRanges, GenomeInfoDb, GenomicRanges |
| LinkingTo | |
| Suggests | knitr, AshkenazimSonChr21 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RareVariantVis_1.6.2.tar.gz |
| Windows Binary | RareVariantVis_1.6.2.zip |
| Mac OS X 10.9 (Mavericks) | RareVariantVis_1.6.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RareVariantVis/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/RareVariantVis/ |
| Package Downloads Report | Download Stats |
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