VariantAnnotation

DOI: 10.18129/B9.bioc.VariantAnnotation  

This is the development version of VariantAnnotation; for the stable release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: Development (3.18)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML	R Script	1. Introduction to VariantAnnotation
HTML	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	1.47.1
In Bioconductor since	BioC 2.9 (R-2.14) (12 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), MatrixGenerics, GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.41.5), SummarizedExperiment(>= 1.19.5), Rsamtools(>= 1.99.0)
Imports	utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), XVector(>= 0.29.2), Biostrings(>= 2.57.2), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.39.7), BSgenome(>= 1.47.3), GenomicFeatures(>= 1.31.3)
LinkingTo	S4Vectors, IRanges, XVector, Biostrings, Rhtslib(>= 1.99.3)
Suggests	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
SystemRequirements	GNU make
Enhances
URL
Depends On Me	alabaster.vcf, annotation, CNVrd2, deepSNV, demuxSNP, ensemblVEP, HelloRanges, HTSeqGenie, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, signeR, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me	AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CNVfilteR, CopyNumberPlots, COSMIC.67, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, epialleleR, fcScan, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, MADSEQ, MMAPPR2, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, scoreInvHap, SigsPack, SNPhood, svaRetro, TitanCNA, tLOH, TVTB, Uniquorn, VCFArray, YAPSA, ZygosityPredictor
Suggests Me	alabaster.files, AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CNVgears, CrispRVariants, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, ldblock, omicsPrint, podkat, RVS, SeqArray, splatter, supersigs, systemPipeR, trackViewer, trio, vtpnet
Links To Me
Build Report

Package Archives

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

Source Package	VariantAnnotation_1.47.1.tar.gz
Windows Binary	VariantAnnotation_1.47.1.zip (64-bit only)
macOS Binary (x86_64)	VariantAnnotation_1.47.1.tgz
macOS Binary (arm64)	VariantAnnotation_1.47.1.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