VariantAnnotation

This is the released version of VariantAnnotation; for the devel version, see VariantAnnotation.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Annotation of Genetic Variants

Bioconductor version: Release (3.23)

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, enter citation("VariantAnnotation")):

Valerie Oberchain, Martin Morgan, Michael Lawrence. VariantAnnotation: Annotation of Genetic Variants. doi:10.18129/B9.bioc.VariantAnnotation, R package version 1.58.0, https://bioconductor.org/packages/VariantAnnotation.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.58.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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, annotation, CNVrd2, deepSNV, demuxSNP, HelloRanges, myvariant, PlasmaMutationDetector, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me	AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CCAFE, ClonalSim, CNVfilteR, CopyNumberPlots, COSMIC.67, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, fcScan, fRagmentomics, G4SNVHunter, GA4GHclient, GenomicFiles, GenVisR, ggbio, gmapR, gpcp, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, MutSeqR, parati, ProteoDisco, RAIDS, scoreInvHap, SEMPLR, signeR, SigsPack, SNPhood, svaRetro, tadar, tLOH, transmogR, TVTB, Uniquorn, UPDhmm, VCFArray, YAPSA, ZygosityPredictor
Suggests Me	alabaster.files, AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, epialleleR, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, igvShiny, ldblock, ldsep, MoBPS, omicsPrint, podkat, polyRAD, Rsamtools, RVS, SeqArray, shiny.gosling, SNPassoc, splatter, supersigs, systemPipeR, trackViewer, trio, updog, vtpnet
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	VariantAnnotation_1.58.0.tar.gz
Windows Binary (x86_64)	VariantAnnotation_1.58.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	VariantAnnotation_1.58.0.tgz
macOS Binary (sonoma-arm64)	VariantAnnotation_1.58.0.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	https://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats