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

VariantAnnotation

Annotation of Genetic Variants

Bioconductor version: 2.13

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>

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, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.8.13
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(>= 1.13.47), IRanges(>= 1.19.36), XVector
Imports	methods, BiocGenerics, IRanges, XVector, Biostrings(>= 2.29.2), Biobase, Rsamtools, AnnotationDbi(>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures(>= 1.13.11), 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, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, VariantTools
Imports Me	customProDB, FunciSNP, ggbio, GGtools, gmapR, HTSeqGenie, R453Plus1Toolbox, SeqArray, VariantTools
Suggests Me	GenomicRanges, gmapR, GWASTools, vtpnet

Package Archives

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

Package Source	VariantAnnotation_1.8.13.tar.gz
Windows Binary	VariantAnnotation_1.8.13.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	VariantAnnotation_1.8.13.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats