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

Annotation of Genetic Variants

Bioconductor version: 3.0

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:

## 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 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
Version 1.12.9
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.40), Rsamtools(>= 1.17.26)
Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.2.3), IRanges(>= 2.0.1), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.9), BSgenome, rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.17.13)
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 ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, Rariant, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantTools
Imports Me biovizBase, COSMIC.67, customProDB, FunciSNP, ggbio, GGtools, gmapR, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, R453Plus1Toolbox, SeqArray, VariantFiltering
Suggests Me GenomicRanges, GWASTools, trio, vtpnet
Build Report

Package Archives

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

Package Source VariantAnnotation_1.12.9.tar.gz
Windows Binary VariantAnnotation_1.12.9.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VariantAnnotation_1.12.9.tgz
Mac OS X 10.9 (Mavericks) VariantAnnotation_1.12.9.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-3.0
Package Short Url http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report Download Stats

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