VariantAnnotation

DOI: 10.18129/B9.bioc.VariantAnnotation    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.8

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

Author: Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]

Maintainer: Valerie Obenchain <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("VariantAnnotation")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantAnnotation")

 

PDF R Script 1. Introduction to VariantAnnotation
PDF R Script 2. Using filterVcf to Select Variants from VCF Files
PDF   Reference Manual
Text   NEWS
Video   Reading VCF data

Details

biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.28.13
In Bioconductor since BioC 2.9 (R-2.14) (7.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.8), SummarizedExperiment(>= 1.9.9), Rsamtools(>= 1.33.6)
Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.17.24), IRanges(>= 2.13.13), XVector(>= 0.19.7), Biostrings(>= 2.47.6), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.39.7), BSgenome(>= 1.47.3), GenomicFeatures(>= 1.31.3)
LinkingTo S4Vectors, IRanges, XVector, Biostrings, Rsamtools
Suggests RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me ampliQueso, annotation, cgdv17, CNVrd2, deepSNV, DOQTL, ensemblVEP, genotypeeval, GoogleGenomics, HelloRanges, HTSeqGenie, igvR, MTseeker, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, Rariant, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, signeR, SomaticSignatures, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me AllelicImbalance, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, COSMIC.67, customProDB, DominoEffect, FunciSNP, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, GGtools, gmapR, gQTLstats, gwascat, gwasurvivr, icetea, ldblock, MADSEQ, methyAnalysis, motifbreakR, MTseekerData, MutationalPatterns, PGA, scoreInvHap, SNPhood, systemPipeR, TitanCNA, TVTB, Uniquorn, YAPSA, yriMulti
Suggests Me AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, omicsPrint, podkat, RVS, SeqArray, trackViewer, trio, vtpnet
Links To Me
Build Report  

Package Archives

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

Source Package VariantAnnotation_1.28.13.tar.gz
Windows Binary VariantAnnotation_1.28.13.zip
Mac OS X 10.11 (El Capitan) VariantAnnotation_1.28.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/VariantAnnotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantAnnotation
Package Short Url http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report Download Stats

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