VariantAnnotation

Annotation of Genetic Variants

Bioconductor version: Release (2.12)

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")

To cite this package in a publication, start R and enter:

    citation("VariantAnnotation")

PDF	R Script	filterVcf Overview
PDF	R Script	Introduction to VariantAnnotation
PDF		Reference Manual
Text		NEWS

biocViews	Annotation, DataImport, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.6.8
In Bioconductor since	BioC 2.9 (R-2.14)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics, GenomicRanges(>= 1.11.29), Rsamtools(>= 1.11.26), IRanges(>= 1.17.4)
Imports	methods, BiocGenerics, IRanges, Biostrings, Biobase, Rsamtools, AnnotationDbi(>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures(>= 1.9.35), DBI, utils
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
System Requirements
URL
Depends On Me	cgdv17, ensemblVEP, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, VariantTools
Imports Me	FunciSNP, ggbio, GGtools, gmapR, HTSeqGenie, R453Plus1Toolbox, VariantTools
Suggests Me	GenomicRanges, gmapR, GWASTools

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