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 2.9 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 2.9

Annotate variants with respect to location and amino acid coding

Author: Michael Lawrence and Valerie Obenchain

Maintainer: Valerie Obenchain <vobencha at fhcrc.org>

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

To install this package, start R and enter:

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

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

browseVignettes("VariantAnnotation")

PDF		VariantAnnotation.pdf
PDF		Reference Manual

biocViews	AnnotationData, DataImport, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.0.5
In Bioconductor since	BioC 2.9 (R-2.14) (4.5 years)
License	Artistic-2.0
Depends	methods, R (>= 2.8.0), GenomicRanges, Biostrings, AnnotationDbi, Rsamtools
Imports	AnnotationDbi, Biobase, BSgenome, GenomicFeatures, IRanges(>= 1.11.17), snpStats, DBI
LinkingTo
Suggests	RUnit, BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, SNPlocs.Hsapiens.dbSNP.20090506, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132
SystemRequirements
Enhances
URL
Depends On Me	PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132
Imports Me
Suggests Me
Build Report

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

Package Source	VariantAnnotation_1.0.5.tar.gz
Windows Binary	VariantAnnotation_1.0.5.zip
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-2.9
Package Short Url	http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats

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