VariantAnnotation

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

Annotation of Genetic Variants

Installation

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

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

Details

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.53.0
In Bioconductor since	BioC 2.9 (R-2.14) (13 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(>= 2.19.1)
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)
System Requirements	GNU make
URL

See More

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, 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, R453Plus1Toolbox, RareVariantVis, seqCAT, signeR, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, VariantTools, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, VariantToolsData, annotation, sequencing, variants, PlasmaMutationDetector, PlasmaMutationDetector2
Imports Me	AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CNVfilteR, CopyNumberPlots, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, fcScan, GA4GHclient, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, MADSEQ, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, RAIDS, scoreInvHap, SigsPack, SNPhood, svaRetro, tadar, TitanCNA, 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, RVS, SeqArray, shiny.gosling, splatter, supersigs, systemPipeR, trackViewer, trio, vtpnet, AshkenazimSonChr21, GeuvadisTranscriptExpr, ldsep, polyRAD, SNPassoc, updog
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	VariantAnnotation_1.53.0.tar.gz
Windows Binary (x86_64)	VariantAnnotation_1.53.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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