VariantAnnotation

DOI: 10.18129/B9.bioc.VariantAnnotation    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.14

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

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

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

Installation

To install this package, start R (version "4.1") 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")

 

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	1.40.0
In Bioconductor since	BioC 2.9 (R-2.14) (10.5 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
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	GNU make
Enhances
URL
Depends On Me	annotation, CNVrd2, deepSNV, ensemblVEP, genotypeeval, 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, CNVfilteR, CopyNumberPlots, COSMIC.67, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, epialleleR, fcScan, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, ldblock, MADSEQ, MMAPPR2, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, scoreInvHap, SigsPack, SNPhood, svaRetro, TitanCNA, tLOH, TVTB, Uniquorn, VCFArray, XCIR, YAPSA
Suggests Me	AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CNVgears, CrispRVariants, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, 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_1.40.0.tar.gz
Windows Binary	VariantAnnotation_1.40.0.zip
macOS 10.13 (High Sierra)	VariantAnnotation_1.40.0.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