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 (2.14)

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

Author: Valerie Obenchain, Martin Morgan, Michael Lawrence with contributions from Stephanie Gogarten.

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

Details

biocViews Annotation, DataImport, Genetics, Homo_sapiens, SNP, Sequencing, Software
Version 1.10.5
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomicRanges(>= 1.13.51), Rsamtools(>= 1.15.5)
Imports IRanges(>= 1.21.43), XVector, Biostrings(>= 2.31.19), Biobase, AnnotationDbi(>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures(>= 1.15.15), DBI, utils, rtracklayer
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
System Requirements
URL
Depends On Me ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, 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, Rariant, SeqArray, SomaticSignatures, VariantFiltering
Suggests Me GenomicRanges, GWASTools, trio, vtpnet

Package Archives

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

Package Source VariantAnnotation_1.10.5.tar.gz
Windows Binary VariantAnnotation_1.10.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VariantAnnotation_1.10.5.tgz
Mac OS X 10.9 (Mavericks) VariantAnnotation_1.10.5.tgz
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