VariantAnnotation

Annotation of Genetic Variants

Bioconductor version: Release (2.11)

Annotate variants with respect to location and amino acid coding

Author: Valerie Obenchain, Martin Morgan, Michael Lawrence

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	Introduction to VariantAnnotation
PDF		Reference Manual
Text		NEWS

biocViews	Annotation, DataImport, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.4.12
In Bioconductor since	BioC 2.9 (R-2.14)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, GenomicRanges(>= 1.9.56), Rsamtools(>= 1.9.4), IRanges(>= 1.15.48)
Imports	methods, BiocGenerics(>= 0.1.0), IRanges, Biobase(>= 2.15.1), Rsamtools(>= 1.9.4), AnnotationDbi(>= 1.17.11), Biostrings(>= 2.25.2), zlibbioc, BSgenome, GenomicFeatures(>= 1.9.35), DBI
Suggests	RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats
System Requirements
URL
Depends On Me	cgdv17, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, VariantTools
Imports Me	FunciSNP, ggbio, GGtools, gmapR, R453Plus1Toolbox, VariantTools
Suggests Me	GenomicRanges, gmapR, GWASTools

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