VariantAnnotation

This is thereleased version of VariantAnnotation; for the devel version, seeVariantAnnotation.

Annotation of Genetic Variants

DOI: 10.18129/B9.bioc.VariantAnnotation

Bioconductor version: Release (3.22)

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

Author: Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb], Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, entercitation("VariantAnnotation")):

Installation

To install this package, start R (version "4.5") and enter:

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

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

Documentation

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

browseVignettes("VariantAnnotation")

1. Introduction to VariantAnnotation	HTML	R Script
2. Using filterVcf to Select Variants from VCF Files	HTML	R Script
ensemblVEP: using the REST API with Bioconductor	HTML	R Script
Reference Manual	PDF
NEWS	Text
	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation,DataImport,Genetics,SNP,Sequencing,Software,VariantAnnotation
Version	1.56.0
In Bioconductor since	BioC 2.9 (R-2.14) (14 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods,BiocGenerics(>= 0.37.0),MatrixGenerics,Seqinfo,GenomicRanges(>= 1.61.1),SummarizedExperiment(>= 1.39.1),Rsamtools(>= 2.25.1)
Imports	utils,DBI,Biobase,S4Vectors(>= 0.27.12),IRanges(>= 2.23.9),XVector(>= 0.29.2),Biostrings(>= 2.77.2),AnnotationDbi(>= 1.27.9),rtracklayer(>= 1.69.1),BSgenome(>= 1.77.1),GenomicFeatures(>= 1.61.4),curl
System Requirements	GNU make
URL

Suggests	GenomeInfoDb,RUnit,AnnotationHub,BSgenome.Hsapiens.UCSC.hg19,TxDb.Hsapiens.UCSC.hg19.knownGene,SNPlocs.Hsapiens.dbSNP144.GRCh37,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,PolyPhen.Hsapiens.dbSNP131,snpStats,ggplot2,BiocStyle,knitr,magick,jsonlite,httr,rjsoncons
Linking To	S4Vectors,IRanges,XVector,Biostrings,Rhtslib(>= 2.99.0)
Enhances
Depends On Me	alabaster.vcf,CNVrd2,deepSNV,demuxSNP,HelloRanges,myvariant,PureCN,RareVariantVis,seqCAT,SomaticSignatures,StructuralVariantAnnotation,svaNUMT,VariantFiltering,VariantTools,PolyPhen.Hsapiens.dbSNP131,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,VariantToolsData,annotation,sequencing,variants,PlasmaMutationDetector
Imports Me	AllelicImbalance,appreci8R,BadRegionFinder,BBCAnalyzer,biovizBase,biscuiteer,cardelino,CCAFE,CNVfilteR,CopyNumberPlots,crisprDesign,DAMEfinder,decompTumor2Sig,DominoEffect,fcScan,G4SNVHunter,GA4GHclient,GenomicFiles,ggbio,gmapR,gwascat,gwasurvivr,icetea,igvR,karyoploteR,katdetectr,lineagespot,motifbreakR,MungeSumstats,musicatk,MutationalPatterns,ProteoDisco,RAIDS,scoreInvHap,signeR,SigsPack,SNPhood,svaRetro,tadar,tLOH,transmogR,TVTB,Uniquorn,UPDhmm,VCFArray,YAPSA,ZygosityPredictor,COSMIC.67,gpcp
Suggests Me	alabaster.files,AnnotationHub,BiocParallel,cellbaseR,CrispRVariants,epialleleR,GenomicDataCommons,GenomicRanges,GenomicScores,GWASTools,igvShiny,ldblock,omicsPrint,podkat,Rsamtools,RVS,SeqArray,splatter,supersigs,systemPipeR,trackViewer,trio,vtpnet,AshkenazimSonChr21,GeuvadisTranscriptExpr,ldsep,MoBPS,polyRAD,SNPassoc,updog
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	VariantAnnotation_1.56.0.tar.gz
Windows Binary (x86_64)	VariantAnnotation_1.56.0.zip
macOS Binary (x86_64)	VariantAnnotation_1.56.0.tgz
macOS Binary (arm64)	VariantAnnotation_1.56.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantAnnotation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantAnnotation
Bioc Package Browser	https://code.bioconductor.org/browse/VariantAnnotation/
Package Short Url	https://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats

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