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>

To install this package, start R and enter:

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

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

Documentation

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 Downloads

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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