To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

In most cases, you don't need to download the package archive at all.

VariantAnnotation

This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 2.11

Annotate variants with respect to location and amino acid coding

Author: Valerie Obenchain, Martin Morgan, Michael Lawrence

Maintainer: Valerie Obenchain <vobencha at fhcrc.org>

Citation (from within R, enter citation("VariantAnnotation")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("VariantAnnotation")
PDF R Script Introduction to VariantAnnotation
PDF Reference Manual
Text NEWS

Details

biocViews Annotation, DataImport, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.4.12
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, GenomicRanges(>= 1.9.56), Rsamtools(>= 1.9.4), IRanges(>= 1.15.48)
Imports methods, BiocGenerics(>= 0.1.0), IRanges, Biobase(>= 2.15.1), Rsamtools(>= 1.9.4), AnnotationDbi(>= 1.17.11), Biostrings(>= 2.25.2), zlibbioc, BSgenome, GenomicFeatures(>= 1.9.35), DBI
LinkingTo IRanges, Biostrings, Rsamtools
Suggests RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats
SystemRequirements
Enhances
URL
Depends On Me cgdv17, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, VariantTools
Imports Me FunciSNP, ggbio, GGtools, gmapR, R453Plus1Toolbox, VariantTools
Suggests Me GenomicRanges, gmapR, GWASTools
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source VariantAnnotation_1.4.12.tar.gz
Windows Binary VariantAnnotation_1.4.12.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-2.11
Package Short Url http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report Download Stats

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