To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

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

VariantAnnotation

 

Annotation of Genetic Variants

Bioconductor version: Release (3.1)

Annotate variants, compute amino acid coding changes, predict coding outcomes

Author: Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]

Maintainer: Valerie Obenchain <vobencha at fhcrc.org>

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

Installation

To install this package, start R and enter:

source("http://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 filterVcf Overview
PDF R Script Introduction to VariantAnnotation
PDF   Reference Manual
Text   NEWS
Video   Reading VCF data

Details

biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.14.6
In Bioconductor since BioC 2.9 (R-2.14) (3.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.19.47), Rsamtools(>= 1.19.52)
Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.5.14), IRanges(>= 2.1.27), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.9), BSgenome, rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.19.17)
LinkingTo S4Vectors, IRanges, XVector, Biostrings, Rsamtools
Suggests RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me AllelicImbalance, ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, GoogleGenomics, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, Rariant, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantFiltering, VariantTools
Imports Me AllelicImbalance, biovizBase, COSMIC.67, customProDB, FunciSNP, ggbio, GGtools, gmapR, gQTLstats, gwascat, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, methyAnalysis, R453Plus1Toolbox, SeqArray, SeqVarTools, systemPipeR
Suggests Me AnnotationHub, GenomicRanges, GWASTools, podkat, trio, vtpnet
Build Report  

Package Archives

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

Package Source VariantAnnotation_1.14.6.tar.gz
Windows Binary VariantAnnotation_1.14.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VariantAnnotation_1.14.6.tgz
Mac OS X 10.9 (Mavericks) VariantAnnotation_1.14.6.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-3.1
Package Short Url http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report Download Stats

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